Biological Markers and Methods for Predicting Response to B-Cell Antagonists

ABSTRACT

Biological markers that predict patient responsiveness to B-cell antagonists are provided. Also provided are methods of using such biological markers. In addition, methods for identifying patients suffering from an autoimmune disease, e.g., rheumatoid arthritis, who are not likely to respond to B-cell antagonists are provided, as are methods of treating such patients. Methods for selecting therapeutic agents to treat such patients are also provided.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of International Application No.PCT/US2012/026774 having an international filing date of Feb. 27, 2012,which claims the benefit of priority of provisional U.S. Application No.61/447,518 filed Feb. 28, 2011 and provisional U.S. Application No.61/527,525 filed Aug. 25, 2011, all of which are hereby incorporated byreference in their entirety.

FIELD

Biological markers that predict patient responsiveness to B-cellantagonists are provided. Also provided are methods of using suchbiological markers. In addition, methods for identifying patientssuffering from an autoimmune disease, e.g., rheumatoid arthritis, whoare not likely to respond to B-cell antagonists are provided, as aremethods of treating such patients. Methods for selecting therapeuticagents to treat such patients are also provided.

BACKGROUND

B lymphocytes play an important role in the pathogenesis of autoimmunediseases. Certain B-cell depleting therapeutic agents have been shown tobe effective for the treatment of various autoimmune diseases, includingfor example, rheumatoid arthritis (RA), multiple sclerosis (MS) andantineutrophil cytoplasmic antibody (ANCA)—associated vasculitis.

B cells mature within the bone marrow and leave the marrow expressing anantigen-binding antibody on their cell surface. When a naïve B cellfirst encounters the antigen for which its membrane-bound antibody isspecific, the cell begins to divide rapidly and its progenydifferentiate into memory B cells and effector cells called plasmablastswhich ultimately differentiate into plasma cells. Memory B cells have alonger life span and continue to express membrane-bound antibody withthe same specificity as the original parent cell. Plasma cells do notproduce membrane-bound antibody, but instead produce the antibody in aform that can be secreted. Secreted antibodies are the major effectormolecules of humoral immunity.

B-cell lymphomas express a cell surface antigen, CD20, and this antigencan serve as a target of therapeutic agents for the treatment of suchlymphomas. In essence, such targeting can be generalized as follows:antibodies specific to the CD20 surface antigen of B cells areadministered to a patient. These anti-CD20 antibodies specifically bindto the CD20 antigen of (ostensibly) both normal and malignant B cells;the antibody bound to the CD20 surface antigen may lead to thedestruction and depletion of neoplastic B cells. Thus, such anti-CD20antibodies are known as B-cell depleting therapeutic agents.

One such anti-CD20 antibody is rituximab (RITUXAN®) antibody, which is agenetically engineered chimeric murine/human monoclonal antibodydirected against the CD20 antigen. Rituximab is the antibody called“C2B8” in U.S. Pat. No. 5,736,137 (Anderson et al.). Rituximab isindicated for the treatment of patients with relapsed or refractorylow-grade or follicular, CD20-positive, B-cell non-Hodgkin's lymphoma.In vitro mechanism-of-action studies have demonstrated that rituximabbinds human complement and lyses lymphoid B-cell lines through CDC (Reffet al., Blood, 83(2):435-445 (1994)). Additionally, it has significantactivity in assays for ADCC. Rituximab is FDA approved for not only fortherapy of diffuse large B cell lymphoma, chronic lymphocytic leukemia,but also for rheumatoid arthritis (RA) patients with previous inadequateresponse to TNF antagonist therapies. Importantly, rituximab sparesCD20-negative early B cell lineage precursor cells and late B lineageplasma cells in the bone marrow, and treated patients usually begin toreplete their peripheral blood B cell pool by 4-6 months.

Rheumatoid arthritis (RA) is a clinically important, chronic systemicautoimmune inflammatory disease affecting between 1.3 and 2.1 millionpersons in the United States (See, e.g., Alamanosa and Drosos,Autoimmun. Rev., 4:130-136 (2005)). RA is an autoimmune disorder ofunknown etiology. Most RA patients suffer a chronic course of diseasethat, even with currently available therapies, may result in progressivejoint destruction, deformity, disability and even premature death. Morethan 9 million physician visits and more than 250,000 hospitalizationsper year result from RA.

Diagnosis of RA typically relies on clinical and laboratory evaluationof a patient's signs and symptoms. Generally, laboratory evaluation of apatient suspected of having RA may include determination of the level ofcertain antibodies in serum known as rheumatoid factor (RF) andantibodies to cyclic citrullinated peptide (anti-CCP). (See, e.g.,Schellekens et al., Arthritis Rheum., 43:155-163 (2000); DiFranco etal., Rev. Rheum. Engl. Ed., 66(5):251-255 (1999); Rantapaa-Dahlqvist etal., Arthritis Rheum., 48:2741-2749 (2003); Li et al., Bioinformatics22(12):1503-1507 (2006); Russell et al., J. Rheumatol., 33(7):1240-1242(2006); Ota, Rinsho byori. Jap. J. Clin. Pathol., 54(8)861-868 (2006);Avouac et al., Ann. Rheum. Dis., 65(7):845-851 (2006)). While theseantibodies are often found in the serum of RA patients, not all RApatients have them. An additional blood test known as the erythrocytesedimentation rate (ESR) may also be used. An elevated ESR indicates thegeneral presence of an inflammatory process, although not necessarilyRA. Further blood tests may be used to assess the level of otherfactors, such as C-reactive protein (CRP), that have been associatedwith RA. In addition, radiographic analysis of affected joints may beperformed. In sum, such currently available laboratory tests to diagnoseRA are imprecise and imperfect.

In certain instances, diagnosis of RA is made if a patient satisfiescertain American College of Rheumatology (ACR) criteria. Certain suchcriteria include morning stiffness in and around the joints lasting forat least 1 hour before maximal improvement; arthritis of three or morejoint areas: at least three joint areas have simultaneously had softtissue swelling or fluid (not bony overgrowth alone) observed by aphysician; the 14 possible joint areas (right and left) are proximalinterphalangeal (PIP), metacarpophalangeal (MCP), wrist, elbow, knee,ankle, and metatarsophalangeal (MTP) joints; arthritis of hand joints:at least one joint area swollen as above in wrist, MCP, or PIP joint;symmetric arthritis: simultaneous involvement of the same joint areas(as in arthritis of three or more joint areas, above) on both sides ofthe body (bilateral involvement of PIP, MCP, or MTP joints is acceptablewithout absolute symmetry); rheumatoid nodules: subcutaneous nodulesover bony prominences or extensor surfaces or in juxta-articular regionsthat are observed by a physician; serum rheumatoid factor: demonstrationof abnormal amounts of serum rheumatoid factor by any method that hasbeen positive in fewer than five percent of normal control patients;radiographic changes: radiographic changes typical of rheumatoidarthritis on posteroanterior hand and wrist X-rays, which must includeerosions or unequivocal bony decalcification localized to or most markedadjacent to the involved joints (osteoarthritis changes alone do notqualify). Diagnosis of RA is typically made if a patient satisfies atleast four of the above criteria.

In certain instances, a diagnosis of RA is made if a patient has aparticular Disease Activity Score (DAS) (see, e.g., Van der Heijde D. M.et al., J Rheumatol, 1993, 20(3): 579-81; Prevoo M. L. et al, ArthritisRheum, 1995, 38: 44-8). The DAS system represents both current state ofdisease activity and change. The DAS scoring system uses a weightedmathematical formula, derived from clinical trials in RA. For example,the DAS 28 is 0.56 (T28)+0.28(SW28)+0.70(Ln ESR)+0.014 GH wherein Trepresents tender joint number, SW is swollen joint number, ESR iserythrocyte sedimentation rate, and GH is global health. Various valuesof the DAS represent high or low disease activity as well as remission,and the change and endpoint score result in a categorization of thepatient by degree of response (none, moderate, good).

Multiple Sclerosis (MS) is an autoimmune demyelinating disorder of thecentral nervous system that affects the brain and spinal cord. MSgenerally exhibits a relapsing-remitting course or a chronic progressivecourse. Relapsing-remitting MS (RRMS) is characterized by partial ortotal recovery after attacks. Secondary-progressive MS (SPMS) is arelapsing-remitting course which becomes steadily progressive. Attacksand partial recoveries may continue to occur. Primary-progressive MS(PPMS) is progressive from the onset. Symptoms in patients with PPMSgenerally do not remit—i.e., decrease in intensity. Current treatmentsfor MS include corticosteroids, beta interferons (BETAFERON®, AVONEX®,REBIF®), glatiramer acetate (COPAXONE®), methotrexate, azathioprine,cyclophosphamide, cladribine, baclofen, tizanidine, amitriptyline,carbamazepine (Berkow et al. (ed.), 1999, supra) and natalizumab(TYSABRI®). In addition, consistent with reports implicating B-cells inthe pathogenesis of MS, rituximab has shown some clinical activity inRRMS (see, e.g., Cross et al., J. Neuroimmunol. 180:63-70 (2006) and inPPMS (see, e.g., Hawker K et al., Ann Neurol. 66(4):460-71 (2009)).

Wegener's granulomatosis and microscopic polyangiitis are classified asantineutrophil cytoplasmic antibody (ANCA)—associated vasculitidesbecause most patients with generalized disease have antibodies againstproteinase 3 or myeloperoxidase. (Jennette J C et al., Arthritis Rheum37:187-192 (1994); Finkielman J D et al., Am J Med 120(7):643.e9-643.14(2007)) The ANCA-associated vasculitides affect small-to-medium-sizeblood vessels, with a predilection for the respiratory tract andkidneys. (Hoffman G S et al., Ann Intern Med 116:488-498 (1992);Guillevin L et al., Arthritis Rheum 42:421-430 (1999); Reinhold-Keller Eet al., Arthritis Rheum 43:1021-1032 (2000); Stone J H. Arthritis Rheum48:2299-2309 (2003)). Cyclophosphamide and glucocorticoids have been thestandard therapy for remission induction for nearly four decades.(Novack S N et al., N Engl J Med 284:938-942 (1971); Fauci A S et al.,Medicine (Baltimore) 52:535-561 (1973)). More recently, a number ofstudies have shown that rituximab demonstrates clinical activity inWegener's granulomatosis and ANCA-vasculitis. (Specks et al. Arthritis &Rheumatism, (12):2836-2840 (2001); Keogh et al., Kidney Blood Press.Res., 26:293 (2003); Eriksson, “Kidney and Blood Pressure Research,26:294 (2003); Jayne et al., Kidney and Blood Pressure Research,26:294-295 (2003); Eriksson, J. Internal Med., 257:540-548 (2005); Keoghet al., Arthritis and Rheumatism, 52:262-268 (2005); Stone et al., N.England J. Med. 363(3):221-231 (2010)).

A number of published studies in RA report the attempted identificationof reliable biomarkers for diagnostic and prognostic purposes, includingbiomarkers that can be used to predict patient responsiveness to varioustherapeutic agents. (See e.g., Rioja et al., Arthritis and Rheum.58(8):2257-2267 (2008); Pyrpasopoulou et al., Mol. Diagn. Ther.14(1):43-48 (2010); WO 2004/0009479; WO 2007/0105133; WO 2007/038501; WO2007/135568; WO 2008/104608; WO 2008/056198; WO 2008/132176; and WO2008/154423). No clinically validated diagnostic markers, however, e.g.,biomarkers, have been identified that enable clinicians or others toaccurately define pathophysiological aspects of rheumatoid arthritis,clinical activity, response to therapy, prognosis, or risk of developingthe disease. Accordingly, as RA patients seek treatment, there isconsiderable trial and error involved in the search for therapeuticagent(s) effective for a particular patient. Such trial and error ofteninvolves considerable risk and discomfort the patient in order to findthe most effective therapy. Thus, there is a need for more effectivemeans for determining which patients will respond to which treatment andfor incorporating such determinations into more effective treatmentregimens for rheumatoid arthritis patients.

It would be highly advantageous to have additional diagnostic methods,including molecular-based diagnostic methods, that can be used toobjectively identify the presence of and/or classify rheumatic diseasein a patient, define pathophysiologic aspects of rheumatoid arthritis,multiple scerlosis or ANCA-vasculitis, as well as clinical activity,response to therapy, including response to treatment with varioustherapeutic agents, prognosis, and/or risk of developing disease. Inaddition, it would be advantageous to have molecular-based diagnosticmarkers associated with various clinical and/or pathophysiologicaland/or other biological indicators of disease. Thus, there is acontinuing need to identify new molecular biomarkers associated withrheumatoid arthritis as well as other autoimmune disorders. Suchassociations would greatly benefit the identification of the presence ofdisease in patients or the determination of susceptibility to developthe disease. Such associations would also benefit the identification ofpathophysiologic aspects of RA, MS, ANCA-vasculitis, clinical activity,response to therapy, or prognosis. In addition, statistically andbiologically significant and reproducible information regarding suchassociations could be utilized as an integral component in efforts toidentify specific subsets of patients who would be expected tosignificantly benefit from treatment with a particular therapeuticagent, for example where the therapeutic agent is or has been shown inclinical studies to be of therapeutic benefit in such specific patientsubpopulation.

The invention described herein meets certain of the above-describedneeds and provides other benefits.

All references cited herein, including patent applications andpublications, are incorporated by reference in their entirety for anypurpose.

SUMMARY

The compositions and methods of the invention are based, at least inpart, on the discovery that elevated baseline blood levels of certainmolecular markers for late B lineage stage plasma/plasmablast cells inRA patients, and in certain embodiments, low baseline blood levels ofcertain molecular markers for naïve/mature B cells in RA patients, arepredictive of responsiveness of RA patients to treatment with B-cellantagonists, e.g., anti-CD20 monoclonal antibodies, and the use of suchmolecular markers, alone or in combination, to predict patientresponsiveness to therapeutic regimens involving B-cell antagonists. Incertain embodiments, such molecular markers, alone or in combination,are predictive of responsiveness of patients suffering from certainother autoimmune diseases, e.g., multiple sclerosis, lupus, andANCA-vasculitis, to treatment with B-cell antagonists.

Accordingly, in one aspect, compositions for predicting the response ofa patient to a therapy comprising a B-cell antagonist are provided. Incertain embodiments, the composition comprises a biomarker comprisingelevated total plasma/plasmablast cell mRNA in a biological sampleobtained from a patient compared to the level of totalplasma/plasmablast cell mRNA in a biological sample obtained from acontrol subject or compared to a threshold value for totalplasma/plasmablast cell mRNA. In certain embodiments, the compositionfurther comprises a biomarker comprising a low level of totalnaïve/mature B cell mRNA in the patient's biological sample compared tothe level of total naïve/mature B cell mRNA in the control subject'sbiological sample or compared to a threshold value for totalnaïve/mature B cell mRNA. In certain embodiments, the biological sampleis whole blood. In certain embodiments, the patient is suffering from,or is suspected of suffering from, rheumatoid arthritis. In certainembodiments, the patient is suffering from, or is suspected of sufferingfrom, multiple sclerosis, lupus, or ANCA-vasculitis. In a furtherembodiment, the patient is suffering from, or is suspected of sufferingfrom, relapsing-remitting multiple sclerosis or primary progressivemultiple sclerosis. In certain embodiments, the B-cell antagonist isselected from an anti-CD22 antibody, an anti-CD20 antibody, an anti-BR3antibody, and a BR3-Fc immunoadhesin. In certain embodiments, the B-cellantagonist is an anti-CD20 antibody. In a further embodiment, theanti-CD20 antibody is selected from rituximab, ibritumomab tiuxetan,tositumomab, ocrelizumab, 1F5, 2H7, and A20. In a still furtherembodiment, the anti-CD20 antibody is rituximab. In yet anotherembodiment, the anti-CD20 antibody is ocrelizumab. In certainembodiments, the response predicted to the therapeutic agent comprisingthe B-cell antagonist is non-response.

In another aspect, the composition comprises a biomarker comprising anelevated expression level of a plasma/plasmablast cell-enriched gene ina biological sample obtained from the patient compared to the expressionlevel of the plasma/plasmablast cell-enriched gene in a biologicalsample obtained from a control subject. In certain embodiments, thecomposition comprises a biomarker comprising an elevated expressionlevel of a plasma/plasmablast cell-enriched gene in a biological sampleobtained from the patient compared to a threshold value for theplasma/plasmablast cell-enriched gene. In certain embodiments, theplasma/plasmablast cell-enriched gene is IgJ. In certain embodiments,the biomarker comprises mRNA. In certain embodiments, the biologicalsample is whole blood. In certain embodiments, the patient is sufferingfrom, or is suspected of suffering from, rheumatoid arthritis. Incertain embodiments, the patient is suffering from, or is suspected ofsuffering from, multiple sclerosis, lupus, or ANCA-vasculitis. In afurther embodiment, the patient is suffering from, or is suspected ofsuffering from, relapsing-remitting multiple sclerosis or primaryprogressive multiple sclerosis. In certain embodiments, the B-cellantagonist is selected from an anti-CD22 antibody, an anti-CD20antibody, an anti-BR3 antibody, and a BR3-Fc immunoadhesin. In certainembodiments, the B-cell antagonist is an anti-CD20 antibody. In afurther embodiment, the anti-CD20 antibody is selected from rituximab,ibritumomab tiuxetan, tositumomab, ocrelizumab, 1F5, 2H7, and A20. In astill further embodiment, the anti-CD20 antibody is rituximab. In yetanother embodiment, the anti-CD20 antibody is ocrelizumab. In certainembodiments, the response predicted to the therapeutic agent comprisingthe B-cell antagonist is non-response.

In yet another aspect, the composition comprises a biomarker comprisinga low expression level of a naïve/mature B cell-enriched gene in apatient's biological sample compared to the expression level of thenaïve/mature B cell-enriched gene in a control subject's biologicalsample. In certain embodiments, the composition comprises a biomarkercomprising a low expression level of a naïve/mature B cell-enriched genein a biological sample obtained from the patient compared to a thresholdvalue for the naïve/mature B cell-enriched gene. In certain embodiments,the naïve/mature B cell-enriched gene is FCRL5. In certain embodiments,the naïve/mature B cell-enriched gene is CD19. In certain embodiments,the biomarker comprises mRNA. In certain embodiments, the biologicalsample is whole blood. In certain embodiments, the patient is sufferingfrom, or is suspected of suffering from, rheumatoid arthritis. Incertain embodiments, the patient is suffering from, or is suspected ofsuffering from, multiple sclerosis, lupus, or ANCA-vasculitis. In afurther embodiment, the patient is suffering from, or is suspected ofsuffering from, relapsing-remitting multiple sclerosis or primaryprogressive multiple sclerosis. In certain embodiments, the B-cellantagonist is selected from an anti-CD22 antibody, an anti-CD20antibody, an anti-BR3 antibody, and a BR3-Fc immunoadhesin. In certainembodiments, the B-cell antagonist is an anti-CD20 antibody. In afurther embodiment, the anti-CD20 antibody is selected from rituximab,ibritumomab tiuxetan, tositumomab, ocrelizumab, 1F5, 2H7, and A20. In astill further embodiment, the anti-CD20 antibody is rituximab. In yetanother embodiment, the anti-CD20 antibody is ocrelizumab. In certainembodiments, the response predicted to the therapeutic agent comprisingthe B-cell antagonist is non-response.

In yet still another aspect, the composition comprises more than onebiomarker. In certain embodiments, the composition comprises a biomarkercomprising an elevated expression level of a plasma/plasmablastcell-enriched gene and a biomarker comprising a low expression level ofa naïve/mature B cell-enriched gene in a patient's biological sample. Incertain embodiments, the expression level of the more than one biomarkerin the patient's biological sample is compared to the expression levelin a control subject's biological sample. In certain embodiments, theexpression level of the more than one biomarker in the patient'sbiological sample is compared to a threshold value for theplasma/plasmablast cell-enriched gene and a threshold value for thenaïve/mature B cell-enriched gene. In certain embodiments, theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is FCRL5. In certain embodiments, theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is CD19. In certain embodiments, the more than onebiomarker comprises mRNA. In certain embodiments, the biological sampleis whole blood. In certain embodiments, the patient is suffering from,or is suspected of suffering from, rheumatoid arthritis. In certainembodiments, the patient is suffering from, or is suspected of sufferingfrom, multiple sclerosis, lupus, or ANCA-vasculitis. In a furtherembodiment, the patient is suffering from, or is suspected of sufferingfrom, relapsing-remitting multiple sclerosis or primary progressivemultiple sclerosis. In certain embodiments, the B-cell antagonist isselected from an anti-CD22 antibody, an anti-CD20 antibody, an anti-BR3antibody, and a BR3-Fc immunoadhesin. In certain embodiments, the B-cellantagonist is an anti-CD20 antibody. In a further embodiment, theanti-CD20 antibody is selected from rituximab, ibritumomab tiuxetan,tositumomab, ocrelizumab, 1F5, 2H7, and A20. In a still furtherembodiment, the anti-CD20 antibody is rituximab. In yet anotherembodiment, the anti-CD20 antibody is ocrelizumab. In certainembodiments, the response predicted to the therapeutic agent comprisingthe B-cell antagonist is non-response.

In another aspect, methods for predicting the response of a patient to atherapy comprising a B-cell antagonist are provided. In certainembodiments, the method comprises measuring in a biological sampleobtained from the patient the expression of at least one gene enrichedin plasma/plasmablast cells and comparing the expression of the at leastone gene in the patient's biological sample to the expression of thesame at least one gene in a biological sample obtained from a controlsubject or to a threshold value for the at least one plasma/plasmablastcell-enriched gene, wherein elevated expression of the at least one genein the patient's biological sample compared to the expression in thecontrol subject's biological sample or to the threshold value ispredictive of response of the patient to the therapy comprising theB-cell antagonist. In certain embodiments, the plasma/plasmablastcell-enriched gene is IgJ. In certain embodiments, measuring theexpression of at least one gene comprises measuring mRNA. In a furtherembodiment, measuring mRNA comprises a PCR method or a microarray chip.In certain embodiments, the biological sample comprises whole blood. Incertain embodiments, the patient is suffering from, or is suspected ofsuffering from, rheumatoid arthritis. In certain embodiments, thepatient is suffering from, or is suspected of suffering from, multiplesclerosis, lupus, or ANCA-vasculitis. In a further embodiment, thepatient is suffering from, or is suspected of suffering from,relapsing-remitting multiple sclerosis or primary progressive multiplesclerosis. In certain embodiments, the B-cell antagonist is selectedfrom an anti-CD22 antibody, an anti-CD20 antibody, an anti-BR3 antibody,and a BR3-Fc immunoadhesin. In certain embodiments, the B-cellantagonist is an anti-CD20 antibody. In a further embodiment, theanti-CD20 antibody is selected from rituximab, ibritumomab tiuxetan,tositumomab, ocrelizumab, 1F5, 2H7, and A20. In a still furtherembodiment, the anti-CD20 antibody is rituximab. In yet anotherembodiment, the anti-CD20 antibody is ocrelizumab. In certainembodiments, the response predicted to the therapeutic agent comprisingthe B-cell antagonist is non-response.

In still another aspect, the method comprises measuring in thebiological sample obtained from the patient the expression of at leastone gene enriched in naïve/mature B cells and comparing the expressionof the at least one naïve/mature B cell-enriched gene in the patient'sbiological sample to the expression of the same at least onenaïve/mature B cell-enriched gene in the biological sample obtained fromthe control subject or to a threshold value for the naïve/mature Bcell-enriched gene, wherein a low level of expression of the at leastone naïve/mature B cell-enriched gene in the patient's biological samplecompared to the expression of the same at least one naïve/mature Bcell-enriched gene in the control subject's biological sample or to thethreshold value for the naïve/mature B cell-enriched gene is predictiveof response of the patient to the therapy comprising the B-cellantagonist. In certain embodiments, the naïve/mature B cell-enrichedgene is FCRL5. In certain embodiments, the naïve/mature B cell-enrichedgene is CD 19. In certain embodiments, measuring the expression of atleast one gene comprises measuring mRNA. In a further embodiment,measuring mRNA comprises a PCR method or a microarray chip. In certainembodiments, the biological sample comprises whole blood. In certainembodiments, the patient is suffering from, or is suspected of sufferingfrom, rheumatoid arthritis. In certain embodiments, the patient issuffering from, or is suspected of suffering from, multiple sclerosis,lupus, or ANCA-vasculitis. In a further embodiment, the patient issuffering from, or is suspected of suffering from, relapsing-remittingmultiple sclerosis or primary progressive multiple sclerosis. In certainembodiments, the B-cell antagonist is selected from an anti-CD22antibody, an anti-CD20 antibody, an anti-BR3 antibody, and a BR3-Fcimmunoadhesin. In certain embodiments, the B-cell antagonist is ananti-CD20 antibody. In a further embodiment, the anti-CD20 antibody isselected from rituximab, ibritumomab tiuxetan, tositumomab, ocrelizumab,1F5, 2H7, and A20. In a still further embodiment, the anti-CD20 antibodyis rituximab. In yet another embodiment, the anti-CD20 antibody isocrelizumab. In certain embodiments, the response predicted to thetherapeutic agent comprising the B-cell antagonist is non-response.

In yet another aspect, the method comprises measuring in a biologicalsample obtained from the patient the expression of at least one geneenriched in plasma/plasmablast cells and the expression of at least onegene enriched in naïve/mature B cells. In certain embodiments, theexpression level of the plasma/plasmablast cell-enriched gene(s) and theexpression level of the naïve/mature B cell-enriched gene(s) in thepatient's biological sample are compared to the expression levels of thesame respective genes in a control subject's biological sample. Incertain embodiments, the expression level of the plasma/plasmablastcell-enriched gene(s) and the expression level of the naïve/mature Bcell-enriched gene(s) in the patient's biological sample are compared tothreshold values for the plasma/plasmablast cell-enriched gene(s) andthe naïve/mature B cell-enriched gene(s), respectively. In certainembodiments, the plasma/plasmablast cell-enriched gene is IgJ and thenaïve/mature B cell-enriched gene is FCRL5. In certain embodiments, theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is CD19. In certain embodiments, measuring geneexpression comprises measuring mRNA. In a further embodiment, measuringmRNA comprises a PCR method or a microarray chip. In certainembodiments, the biological sample comprises whole blood. In certainembodiments, the patient is suffering from, or is suspected of sufferingfrom, rheumatoid arthritis. In certain embodiments, the patient issuffering from, or is suspected of suffering from, multiple sclerosis,lupus, or ANCA-vasculitis. In a further embodiment, the patient issuffering from, or is suspected of suffering from, relapsing-remittingmultiple sclerosis or primary progressive multiple sclerosis. In certainembodiments, the B-cell antagonist is selected from an anti-CD22antibody, an anti-CD20 antibody, an anti-BR3 antibody, and a BR3-Fcimmunoadhesin. In certain embodiments, the B-cell antagonist is ananti-CD20 antibody. In a further embodiment, the anti-CD20 antibody isselected from rituximab, ibritumomab tiuxetan, tositumomab, ocrelizumab,1F5, 2H7, and A20. In a still further embodiment, the anti-CD20 antibodyis rituximab. In yet another embodiment, the anti-CD20 antibody isocrelizumab. In certain embodiments, the response predicted to thetherapeutic agent comprising the B-cell antagonist is non-response.

In another aspect, methods of treating autoimmune diseases in patientscomprising administering a therapeutically effective amount of atherapeutic agent other than a B-cell antagonist are provided. Incertain embodiments, a biological sample obtained from the patient priorto treatment has been shown to possess elevated expression of at leastone gene enriched in plasma/plasmablast cells compared to the expressionlevel of the same at least one gene in a biological sample obtained froma control subject or to a threshold value for the plasma/plasmablastcell-enriched gene. In certain embodiments, the biological sample has inaddition been shown to possess a low level of expression of at least onegene enriched in naïve/mature B cells compared to the expression levelof the same at least one gene enriched in naïve/mature B cells in thebiological sample obtained from the control subject or to a thresholdvalue for the naïve/mature B cell-enriched gene. In certain embodiments,the plasma/plasmablast cell-enriched gene is IgJ. In certainembodiments, the naïve/mature B cell-enriched gene is FCRL5. In certainembodiments, the naïve/mature B cell-enriched gene is CD19. In certainembodiments, the plasma/plasmablast cell-enriched gene is IgJ and thenaïve/mature B cell-enriched gene is FCRL5. In certain embodiments, theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is CD19. In certain embodiments, the biologicalsample comprises whole blood. In certain embodiments, the autoimmunedisease is rheumatoid arthritis, multiple sclerosis, relapsing-remittingmultiple sclerosis, primary progressive multiple sclerosis, lupus, orANCA-vasculitis.

In one aspect, gene expression is measured by microarray. In anotheraspect gene expression is measured by polymerase chain reaction (PCR) orreal-time quantitative polymerase chain reaction (qPCR). In anotheraspect, gene expression is measured by multiplex-PCR. According toanother embodiment, expression of a gene of interest in a patient'sbiological sample is considered elevated when compared to that of acontrol subject's biological sample if the relative mRNA level of thegene of interest in the patient's sample is greater than 2 fold of thelevel of the control subject's mRNA. According to another embodiment,the relative mRNA level of the gene of interest in the patient's sampleis greater than 3 fold, 5 fold, 10 fold, 15 fold, 20 fold, 25 fold, or30 fold compared to the level in the control subject's sample. Inanother embodiment, expression of a gene of interest in a patient'sbiological sample is considered low when compared to that of a controlsubject's biological sample if the relative mRNA level of the gene ofinterest in the patient's sample is less than 2 fold of the level of thecontrol subject's mRNA. According to another embodiment, expression of agene of interest in a patient's biological sample is considered low whencompared to that of a control subject's biological sample if therelative mRNA level of the gene of interest in the patient's sample isless than 3 fold, 5 fold, 10 fold, 15 fold, 20 fold, 25 fold, or 30 foldcompared to the level in the control subject's sample.

In another aspect, the gene expression level is measured by a PCR methodor a microarray method. In one embodiment, the microarray methodcomprises the use of a microarray chip having one or more nucleic acidmolecules that can hybridize under stringent conditions to a nucleicacid molecule encoding a gene mentioned above. In one embodiment, thePCR method is qPCR. In one embodiment, the PCR method is multiplex-PCR.

In yet another aspect, methods of a selecting a therapeutic agent fortreatment of a patient suffering from an autoimmune disease areprovided. In certain embodiments, the method comprises obtaining abiological sample from the patient; measuring in the biological sampleobtained from the patient the expression of at least one gene enrichedin plasma/plasmablast cells; comparing the expression of the at leastone gene in the patient's biological sample to the expression of thesame at least one gene in a biological sample obtained from a controlsubject or to a threshold value for the at least one plasma/plasmablastcell-enriched gene; determining whether the expression of the at leastone gene in the patient's biological sample is elevated compared to theexpression in the control subject's biological sample or to thethreshold value; and selecting a therapeutic agent other than a B-cellantagonist provided the expression of the at least one gene in thepatient's biological sample is elevated. In a further embodiment, themethod comprises measuring in the biological sample obtained from thepatient the expression of at least one gene enriched in naïve/mature Bcells; comparing the expression of the at least one naïve/mature Bcell-enriched gene in the patient's biological sample to the expressionof the same at least one naïve/mature B cell-enriched gene in thebiological sample obtained from the control subject or to a thresholdvalue for the naïve/mature B cell-enriched gene; determining whether theexpression of the at least one naïve/mature B cell-enriched gene in thepatient's biological sample is low compared to the expression in thesame at least one naïve/mature B cell-enriched gene in the controlsubject's biological sample or to the threshold value for thenaïve/mature B cell-enriched gene; and selecting a therapeutic agentother than a B-cell antagonist provided the expression of the at leastone naïve/mature B cell-enriched gene is low. In certain embodiments,the plasma/plasmablast cell-enriched gene is IgJ. In certainembodiments, the naïve/mature B cell-enriched gene is FCRL5. In certainembodiments, the naïve/mature B cell-enriched gene is CD 19. In certainembodiments, the plasma/plasmablast cell-enriched gene is IgJ and thenaïve/mature B cell-enriched gene is FCRL5. In certain embodiments, theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is CD19. In certain embodiments, measuring geneexpression comprises measuring mRNA. In a further embodiment, measuringmRNA comprises a PCR method or a microarray chip. In certainembodiments, the biological sample comprises whole blood. In certainembodiments, the autoimmune disease is selected from rheumatoidarthritis, multiple sclerosis, relapsing-remitting multiple sclerosis,primary progressive multiple sclerosis, lupus, and ANCA-vasculitis.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows blood mRNA biomarkers for B cells and plasmablasts asdescribed in Example 1. (A) CD19 positive B cells in blood (y axis;cells/μl) compared to CD20 mRNA expression levels (x axis); (B)correlation coefficients between RT-qPCR expression levels ofplasmablast and mature B cell markers and various B cell subsets; theshading bar at the bottom indicates relative expression level from low(left side) to high (right side); (C) Pearson correlation coefficientfor IgJ expression levels (RT-qPCR; y axis) compared to whole genomemRNA microarray analysis (x axis) in whole blood RNA from patientsreceiving rituximab at baseline, day 15 and day 84; (D) comparison ofbaseline IgJ mRNA levels in ACR50 nonresponders (left side) andresponders (right side); the dotted line indicates the 0.1 expressionunit threshold; individuals with IgJ levels above the 0.1 expressionunit threshold are shown as open circles (ACR50 nonresponders, leftside) and open squares (ACR50 responders, right side).

FIG. 2 shows ACR50 response rates in patient groups from the REFLEXtrial, stratified based on the baseline expression of single biomarkersCD19 (A), FCRL5 (B) and combination biomarker IgJ^(hi)CD19^(lo) (C) asdescribed in Example 1. Hatched bars (A-C), ACR50 response rates at 6months (day 168) for patients treated with rituximab; open bars (A-C)ACR50 response rates at 6 months (day 168) for patients that receivedplacebo. The horizontal lines above the bars in panels A-C refer to thesummary statistics calculated for the ACR50 percentage difference forthe active rituximab arm and placebo arm between the biomarker positiveand negative subgroups. P values were calculated using the Fisher exacttest. “n” refers to the number of individual patients in each subgroup.In these experiments, the threshold values were: IgJ expression≧0.1,FCRL5 expression≧0.02, and CD19≧0.05. The IgJ^(hi)CD19^(lo) subgroup (C)had IgJ expression≧0.1 and CD19 expression<0.05.

FIG. 3 shows IgJ biomarker in mRNA samples from patients followinganti-CD20 therapy or placebo as described in Example 1. (A) IgJbiomarker in baseline mRNA samples from the REFLEX (rituximab) trial;(B) IgJ biomarker in baseline mRNA samples from the DANCER (rituximab)trial; (C) IgJ biomarker in baseline mRNA samples from the SERENE(rituximab) trial; (D) IgJ biomarker in baseline mRNA samples from theSCRIPT (ocrelizumab) trial; (E) Odds ratios and 95% c.i. for theenrichment of ACR50 responses in the IgJ^(lo) subgroup as compared tothe IgJ^(hi) subgroup for the individual trials, the replication trialsin aggregate (DANCER, SERENE and SCRIPT), and for all trials together.

FIG. 4 shows IgJ/FCRL5 biomarkers in mRNA samples from patientsfollowing anti-CD20 therapy or placebo as described in Example 1. (A)IgJ^(hi)FCRL5^(lo) biomarkers in baseline mRNA samples from the REFLEXtrial; (B) IgJ^(hi)FCRL5^(lo) biomarkers in baseline mRNA samples fromthe DANCER trial; (C) IgJ^(hi)FCRL5^(lo) biomarkers in baseline mRNAsamples from the SERENE trial; (D) FCRL5^(lo) biomarkers in baselinemRNA samples from the SCRIPT trial. (E) Odds ratios and 95% C.I. for theenrichment of ACR50 responses in the IgJ^(hi)FCRL5^(lo) subgroup ascompared to remaining patients for the individual trials, thereplication trials in aggregate (DANCER, SERENE and SCRIPT), and for alltrials together.

FIG. 5 shows ACR20 (A, D), ACR70 (B, E) and Δ DAS28 (C, F) resultsstratified by the IgJ (A-C) and IgJ^(hi)FCRL5^(lo) (D-F) biomarkersacross all trials as described in Example 1.

FIG. 6 shows baseline IgJ mRNA levels assayed by RT-qPCR in the SCRIPTocrelizumab trial as described in Example 1.

DETAILED DESCRIPTION

Unless defined otherwise, technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Singleton et al., Dictionary ofMicrobiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York,N.Y. 1994), and March, Advanced Organic Chemistry Reactions, Mechanismsand Structure 4th ed., John Wiley & Sons (New York, N.Y. 1992), provideone skilled in the art with a general guide to many of the terms used inthe present application.

CERTAIN DEFINITIONS

For purposes of interpreting this specification, the followingdefinitions will apply and whenever appropriate, terms used in thesingular will also include the plural and vice versa. In the event thatany definition set forth below conflicts with any document incorporatedherein by reference, the definition set forth below shall control.

As used in this specification and the appended claims, the singularforms “a,” “an” and “the” include plural referents unless the contextclearly dictates otherwise. Thus, for example, reference to “a protein”includes a plurality of proteins; reference to “a cell” includesmixtures of cells, and the like.

The term “autoimmune disease” refers to a disease or disorder arisingfrom and/or directed against an individual's own tissues or organs, or aco-segregate or manifestation thereof, or resulting condition therefrom.Typically, various clinical and laboratory markers of autoimmunediseases may exist including, but not limited to,hypergammaglobulinemia, high levels of autoantibodies, antigen-antibodycomplex deposits in tissues, clinical benefit from corticosteroid orimmunosuppressive treatments, and lymphoid cell aggregates in affectedtissues.

“Rheumatoid arthritis,” (RA) refers to a chronic systemic autoimmuneinflammatory disease that mainly involves the synovial membrane ofmultiple joints with resultant injury to the articular cartilage,resulting in joint destruction. The main presenting symptoms in RA arepain, stiffness, swelling, and/or loss of function of one or morejoints.

“Multiple sclerosis” (MS) is an autoimmune demyelinating disorder. MSgenerally exhibits a relapsing-remitting course or a chronic progressivecourse.

As used herein, “relapsing-remitting MS” (RRMS) is characterized bypartial or total recovery after attacks.

The term “secondary-progressive MS” (SPMS) refers to arelapsing-remitting course of MS which becomes steadily progressive.Attacks and partial recoveries may continue to occur.

The term “primary-progressive MS” (PPMS) refers to MS that isprogressive from the onset. Symptoms in patients with PPMS generally donot remit—i.e., decrease in intensity.

The term “polynucleotide” or “nucleic acid,” as used interchangeablyherein, refers to polymers of nucleotides of any length, and include DNAand RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides,modified nucleotides or bases, and/or their analogs, or any substratethat can be incorporated into a polymer by DNA or RNA polymerase. Apolynucleotide may comprise modified nucleotides, such as methylatednucleotides and their analogs. If present, modification to thenucleotide structure may be imparted before or after assembly of thepolymer. The sequence of nucleotides may be interrupted bynon-nucleotide components. A polynucleotide may be further modifiedafter polymerization, such as by conjugation with a labeling component.Other types of modifications include, for example, “caps”, substitutionof one or more of the naturally occurring nucleotides with an analog,internucleotide modifications such as, for example, those with unchargedlinkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates,cabamates, etc.) and with charged linkages (e.g., phosphorothioates,phosphorodithioates, etc.), those containing pendant moieties, such as,for example, proteins (e.g., nucleases, toxins, antibodies, signalpeptides, poly-L-lysine, etc.), those with intercalators (e.g.,acridine, psoralen, etc.), those containing chelators (e.g., metals,radioactive metals, boron, oxidative metals, etc.), those containingalkylators, those with modified linkages (e.g., alpha anomeric nucleicacids, etc.), as well as unmodified forms of the polynucleotide(s).Further, any of the hydroxyl groups ordinarily present in the sugars maybe replaced, for example, by phosphonate groups, phosphate groups,protected by standard protecting groups, or activated to prepareadditional linkages to additional nucleotides, or may be conjugated tosolid supports. The 5′ and 3′ terminal OH can be phosphorylated orsubstituted with amines or organic capping groups moieties of from 1 to20 carbon atoms. Other hydroxyls may also be derivatized to standardprotecting groups. Polynucleotides can also contain analogous forms ofribose or deoxyribose sugars that are generally known in the art,including, for example, 2′-O-methyl-2′-O-allyl, 2′-fluoro- or2′-azido-ribose, carbocyclic sugar analogs, α-anomeric sugars, epimericsugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanosesugars, sedoheptuloses, acyclic analogs and abasic nucleoside analogssuch as methyl riboside. One or more phosphodiester linkages may bereplaced by alternative linking groups. These alternative linking groupsinclude, but are not limited to, embodiments wherein phosphate isreplaced by P(O)S (“thioate”), P(S)S (“dithioate”), “(O)NR 2(“amidate”), P(O)R, P(O)OR′, CO or CH 2 (“formacetal”), in which each Ror R′ is independently H or substituted or unsubstituted alkyl (1-20 C)optionally containing an ether (—O—) linkage, aryl, alkenyl, cycloalkyl,cycloalkenyl or araldyl. Not all linkages in a polynucleotide need beidentical. The preceding description applies to all polynucleotidesreferred to herein, including RNA and DNA.

“Oligonucleotide,” as used herein, refers to short, single strandedpolynucleotides that are at least about seven nucleotides in length andless than about 250 nucleotides in length. Oligonucleotides may besynthetic. The terms “oligonucleotide” and “polynucleotide” are notmutually exclusive. The description above for polynucleotides is equallyand fully applicable to oligonucleotides.

The term “primer” refers to a single stranded polynucleotide that iscapable of hybridizing to a nucleic acid and allowing the polymerizationof a complementary nucleic acid, generally by providing a free 3′-OHgroup.

The term “array” or “microarray” refers to an ordered arrangement ofhybridizable array elements, preferably polynucleotide probes (e.g.,oligonucleotides), on a substrate. The substrate can be a solidsubstrate, such as a glass slide, or a semi-solid substrate, such asnitrocellulose membrane.

The term “amplification” refers to the process of producing one or morecopies of a reference nucleic acid sequence or its complement.Amplification may be linear or exponential (e.g., PCR). A “copy” doesnot necessarily mean perfect sequence complementarity or identityrelative to the template sequence. For example, copies can includenucleotide analogs such as deoxyinosine, intentional sequencealterations (such as sequence alterations introduced through a primercomprising a sequence that is hybridizable, but not fully complementary,to the template), and/or sequence errors that occur duringamplification.

The term “detection” includes any means of detecting, including directand indirect detection.

“Elevated expression” or “elevated levels” refers to an increasedexpression of a mRNA or a protein in a patient relative to a control,such as an individual or individuals who are not suffering from anautoimmune disease, e.g., RA, or relative to a pre-established thresholdor cut-off value.

The term “multiplex-PCR” refers to a single PCR reaction carried out onnucleic acid obtained from a single source (e.g., a patient) using morethan one primer set for the purpose of amplifying two or more DNAsequences in a single reaction.

As used herein, “rheumatoid factor,” or “RF,” refers to IgM, IgG, or IgAisotypes, singly or in any combination, of antibodies detected inpatient serum and directed to antigenic determinants present on humanand animal IgG.

The term “positive for RF” refers to a result of an assay for RF, e.g.,an ELISA assay, where the result is above a threshold or cutoff valuefor that assay for samples that are considered to reproducibly containdetectable levels of RF.

The term “negative for RF” refers to a result of an assay for RF, e.g.,an ELISA assay, where the result is at or below a threshold or cutoffvalue for that assay for samples that are considered to reproduciblycontain undetectable levels of RF.

“Stringency” of hybridization reactions is readily determinable by oneof ordinary skill in the art, and generally is an empirical calculationdependent upon probe length, washing temperature, and saltconcentration. In general, longer probes require higher temperatures forproper annealing, while shorter probes need lower temperatures.Hybridization generally depends on the ability of denatured DNA toreanneal when complementary strands are present in an environment belowtheir melting temperature. The higher the degree of desired homologybetween the probe and hybridizable sequence, the higher the relativetemperature which can be used. As a result, it follows that higherrelative temperatures would tend to make the reaction conditions morestringent, while lower temperatures less so. For additional details andexplanation of stringency of hybridization reactions, see Ausubel etal., Current Protocols in Molecular Biology, Wiley IntersciencePublishers, (1995).

“Stringent conditions” or “high stringency conditions”, as definedherein, can be identified by those that: (1) employ low ionic strengthand high temperature for washing, for example 0.015 M sodiumchloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50 C;(2) employ during hybridization a denaturing agent, such as formamide,for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1%Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5with 750 mM sodium chloride, 75 mM sodium citrate at 42 C; or (3)overnight hybridization in a solution that employs 50% formamide, 5×SSC(0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8),0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon spermDNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42 C, with a 10minute wash at 42 C in 0.2×SSC (sodium chloride/sodium citrate) followedby a 10 minute high-stringency wash consisting of 0.1×SSC containingEDTA at 55 C.

“Moderately stringent conditions” can be identified as described bySambrook et al., Molecular Cloning: A Laboratory Manual, New York: ColdSpring Harbor Press, 1989, and include the use of washing solution andhybridization conditions (e.g., temperature, ionic strength and % SDS)less stringent that those described above. An example of moderatelystringent conditions is overnight incubation at 37° C. in a solutioncomprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate),50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextransulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed bywashing the filters in 1×SSC at about 37-50 C. The skilled artisan willrecognize how to adjust the temperature, ionic strength, etc. asnecessary to accommodate factors such as probe length and the like.

The term “biomarker” as used herein refers to an indicator of aphenotype of a patient, e.g, a pathological state or likelyresponsivenss to a therapeutic agent, which can be detected in abiological sample of the patient. Biomarkers include, but are notlimited to, DNA, RNA, protein, carbohydrate, or glycolipid-basedmolecular markers.

The term “diagnosis” is used herein to refer to the identification orclassification of a molecular or pathological state, disease orcondition. For example, “diagnosis” may refer to identification of aparticular type of RA. “Diagnosis” may also refer to the classificationof a particular subtype of RA, e.g., by histopathological criteria(e.g., lymphoid infiltration or follicle-like lymphoid cluster), or bymolecular features (e.g., a subtype characterized by expression of oneor a combination of particular genes or proteins encoded by said genes).

The term “aiding diagnosis” is used herein to refer to methods thatassist in making a clinical determination regarding the presence, ornature, of a particular type of symptom or condition. For example, amethod of aiding diagnosis of RA can comprise measuring the expressionof certain genes in a biological sample from an individual.

The term “prognosis” is used herein to refer to the prediction of thelikelihood of autoimmune disorder-attributable disease symptoms of anautoimmune disease such as RA.

The term “prediction” is used herein to refer to the likelihood that apatient will respond either favorably or unfavorably to a drug(therapeutic agent) or set of drugs or a therapeutic regimen. In oneembodiment, the prediction relates to the extent of those responses. Inone embodiment, the prediction relates to whether and/or the probabilitythat a patient will survive or improve following treatment, for exampletreatment with a particular therapeutic agent, or for a certain periodof time without disease recurrence. The predictive methods of theinvention can be used clinically to make treatment decisions by choosingthe most appropriate treatment modalities for any particular patient.The predictive methods of the present invention are valuable tools inpredicting if a patient is likely to respond favorably to a treatmentregimen, such as a given therapeutic regimen, including for example,administration of a given therapeutic agent or combination, surgicalintervention, steroid treatment, etc., or whether long-term survival ofthe patient, following a therapeutic regimen is likely.

As used herein, “treatment” refers to clinical intervention in anattempt to alter the natural course of the individual or cell beingtreated, and can be performed before or during the course of clinicalpathology. Desirable effects of treatment include preventing theoccurrence or recurrence of a disease or a condition or symptom thereof,alleviating a condition or symptom of the disease, diminishing anydirect or indirect pathological consequences of the disease, decreasingthe rate of disease progression, ameliorating or palliating the diseasestate, and achieving remission or improved prognosis. In someembodiments, methods and compositions of the invention are useful inattempts to delay development of a disease or disorder.

An “effective amount” refers to an amount effective, at dosages and forperiods of time necessary, to achieve the desired therapeutic orprophylactic result. A “therapeutically effective amount” of atherapeutic agent may vary according to factors such as the diseasestate, age, sex, and weight of the individual, and the ability of theantibody to elicit a desired response in the individual. Atherapeutically effective amount is also one in which any toxic ordetrimental effects of the therapeutic agent are outweighed by thetherapeutically beneficial effects. A “prophylactically effectiveamount” refers to an amount effective, at dosages and for periods oftime necessary, to achieve the desired prophylactic result. Typicallybut not necessarily, since a prophylactic dose is used in subjects priorto or at an earlier stage of disease, the prophylactically effectiveamount will be less than the therapeutically effective amount.

An “individual,” “subject” or “patient” is a vertebrate. In certainembodiments, the vertebrate is a mammal. Mammals include, but are notlimited to, primates (including human and non-human primates) androdents (e.g., mice and rats). In certain embodiments, a mammal is ahuman.

A “control subject” refers to a healthy subject who has not beendiagnosed as having a particular disease, e.g., RA, and who does notsuffer from any sign or symptom associated with that disease.

The term “sample,” as used herein, refers to a composition that isobtained or derived from a subject of interest that contains a cellularand/or other molecular entity that is to be characterized and/oridentified, for example based on physical, biochemical, chemical and/orphysiological characteristics. For example, the phrase “disease sample”and variations thereof refers to any sample obtained from a subject ofinterest that would be expected or is known to contain the cellularand/or molecular entity that is to be characterized.

By “tissue” or “cell sample” is meant a collection of similar cellsobtained from a tissue of a subject or patient. The source of the tissueor cell sample may be solid tissue as from a fresh, frozen and/orpreserved organ or tissue sample or biopsy or aspirate; blood or anyblood constituents; bodily fluids such as cerebral spinal fluid,amniotic fluid, peritoneal fluid, or interstitial fluid; cells from anytime in gestation or development of the subject. The tissue sample mayalso be primary or cultured cells or cell lines. Optionally, the tissueor cell sample is obtained from a disease tissue/organ. The tissuesample may contain compounds which are not naturally intermixed with thetissue in nature such as preservatives, anticoagulants, buffers,fixatives, nutrients, antibiotics, or the like. A “reference sample”,“reference cell”, “reference tissue”, “control sample”, “control cell”,or “control tissue”, as used herein, refers to a sample, cell or tissueobtained from a source known, or believed, not to be afflicted with thedisease or condition for which a method or composition of the inventionis being used to identify. In one embodiment, a reference sample,reference cell, reference tissue, control sample, control cell, orcontrol tissue is obtained from a healthy part of the body of the samesubject or patient in whom a disease or condition is being identifiedusing a composition or method of the invention. In one embodiment, areference sample, reference cell, reference tissue, control sample,control cell, or control tissue is obtained from a healthy part of thebody of an individual who is not the subject or patient in whom adisease or condition is being identified using a composition or methodof the invention.

For the purposes herein a “section” of a tissue sample is meant a singlepart or piece of a tissue sample, e.g. a thin slice of tissue or cellscut from a tissue sample. It is understood that multiple sections oftissue samples may be taken and subjected to analysis according to thepresent invention, provided that it is understood that the presentinvention comprises a method whereby the same section of tissue sampleis analyzed at both morphological and molecular levels, or is analyzedwith respect to both protein and nucleic acid.

By “correlate” or “correlating” is meant comparing, in any way, theperformance and/or results of a first analysis or protocol with theperformance and/or results of a second analysis or protocol. Forexample, one may use the results of a first analysis or protocol incarrying out a second protocols and/or one may use the results of afirst analysis or protocol to determine whether a second analysis orprotocol should be performed. With respect to the embodiment of geneexpression analysis or protocol, one may use the results of the geneexpression analysis or protocol to determine whether a specifictherapeutic regimen should be performed.

A “medicament” is an active drug to treat a disease, disorder, and/orcondition.

The term “increased resistance” to a particular therapeutic agent ortreatment option, when used in accordance with the invention, meansdecreased response to a standard dose of the drug or to a standardtreatment protocol.

The term “decreased sensitivity” to a particular therapeutic agent ortreatment option, when used in accordance with the invention, meansdecreased response to a standard dose of the agent or to a standardtreatment protocol, where decreased response can be compensated for (atleast partially) by increasing the dose of agent, or the intensity oftreatment.

“Patient response” or “response” can be assessed using any endpointindicating a benefit to the patient, including, without limitation, (1)inhibition, to some extent, of disease progression, including slowingdown and complete arrest; (2) reduction in the number of diseaseepisodes and/or symptoms; (3) reduction in lesional size; (4) inhibition(i.e., reduction, slowing down or complete stopping) of disease cellinfiltration into adjacent peripheral organs and/or tissues; (5)inhibition (i.e. reduction, slowing down or complete stopping) ofdisease spread; (6) decrease of auto-immune response, which may, butdoes not have to, result in the regression or ablation of the diseaselesion; (7) relief, to some extent, of one or more symptoms associatedwith the disorder; (8) increase in the length of disease-freepresentation following treatment; and/or (9) decreased mortality at agiven point of time following treatment.

The term “gene signature” is used interchangeably with “gene expressionsignature” and refers to one or a combination of genes whose expressionis indicative of a particular subtype or disease state characterized bycertain molecular, pathological, histological, and/or clinical features.In certain embodiments, a gene expression signature is predictive ofpatient responsiveness to a particular therapeutic agent or treatmentregimen. In certain embodiments, the expression of one or more genescomprising the gene signature is elevated compared to that in controlsubjects. In certain embodiments, the expression of one or more genescomprising the gene signature is decreased compared to that in controlsubjects. In certain embodiments, the expression of one or more genescomprising the gene signature is differentially regulated in testsubjects (e.g., patients) compared to the expression of those gene(s) incontrol subjects.

The term “protein signature” is used interchangeably with “proteinexpression signature” and refers to one or a combination of proteinswhose expression is indicative of a particular subtype or disease statecharacterized by certain molecular, pathological, histological, and/orclinical features. In certain embodiments, a protein expressionsignature is predictive of patient responsiveness to a particulartherapeutic agent or treatment regimen. In certain embodiments, theexpression of one or more proteins comprising the protein signature iselevated compared to that in control subjects. In certain embodiments,the expression of one or more proteins comprising the protein signatureis decreased compared to that in control subjects. In certainembodiments, the expression of one or more proteins comprising theprotein signature is differentially regulated in test subjects (e.g.,patients) compared to the expression of those protein(s) in controlsubjects.

A “RA therapeutic agent,” a “therapeutic agent effective to treat RA,”and grammatical variations thereof, as used herein, refer to an agentthat when provided in an effective amount is known, clinically shown, orexpected by clinicians to provide a therapeutic benefit in a subject whohas RA.

An “MS therapeutic agent,” a “therapeutic agent effective to treat MS,”and grammatical variations thereof, as used herein, refer to an agentthat when provided in an effective amount is known, clinically shown, orexpected by clinicians to provide a therapeutic benefit in a subject whohas MS.

An “ANCA-vaculitis therapeutic agent,” a “therapeutic agent effective totreat ANCA-vasculitis,” and grammatical variations thereof, as usedherein, refer to an agent that when provided in an effective amount isknown, clinically shown, or expected by clinicians to provide atherapeutic benefit in a subject who has ANCA-vasculitis.

A “B-cell surface marker” or “B-cell surface antigen” herein is anantigen expressed on the surface of a B cell that can be targeted withan antagonist that binds thereto. Exemplary B-cell surface markersinclude the CD10, CD19, CD20 (MS4A1), CD21, CD22, CD23, CD24, CD37,CD40, CD53, CD72, CD73, CD74, CDw75, CDw76, CD77, CDw78, CD79a, CD79b,CD80, CD81, CD82, CD83, CDw84, CD85, and CD86 leukocyte surface markers(for descriptions, see The Leukocyte Antigen Facts Book, 2nd Edition.1997, ed. Barclay et al. Academic Press, Harcourt Brace & Co., NewYork). Other B-cell surface markers include RP105, FcRH2, B-cell CR2,CCR6, P2×5, HLA-DOB, CXCR5, FCER2, BR3, Btig, NAG14, SLGC16270, FcRH1,IRTA2, ATWD578, FcRH3, IRTA1, FcRH6, BCMA, and 239287. The B-cellsurface marker of particular interest is preferentially expressed on Bcells compared to other non-B-cell tissues of a mammal and may beexpressed on both precursor B cells and mature B cells.

An “antibody that binds to a B-cell surface marker” is a molecule that,upon binding to a B-cell surface marker, destroys or depletes B cells ina mammal and/or interferes with one or more B-cell functions, e.g. byreducing or preventing a humoral response elicited by the B cell. Theantibody in certain instances is able to deplete B cells (i.e. reducecirculating B-cell levels) in a mammal treated therewith. Such depletionmay be achieved via various mechanisms such as antibody-dependentcell-mediated cytotoxicity (ADCC) and/or complement-dependentcytotoxicity (CDC), inhibition of B-cell proliferation, and/or inductionof B-cell death (e.g. via apoptosis).

An “antagonist” refers to a molecule capable of neutralizing, blocking,inhibiting, abrogating, reducing or interfering with the activities of aparticular or specified protein, including its binding to one or morereceptors in the case of a ligand or binding to one or more ligands incase of a receptor. Antagonists include antibodies and antigen-bindingfragments thereof, proteins, peptides, glycoproteins, glycopeptides,glycolipids, polysaccharides, oligosaccharides, nucleic acids,bioorganic molecules, peptidomimetics, pharmacological agents and theirmetabolites, transcriptional and translation control sequences, and thelike. Antagonists also include small molecule inhibitors of the protein,and fusion proteins, receptor molecules and derivatives which bindspecifically to the protein thereby sequestering its binding to itstarget, antagonist variants of the protein, antisense molecules directedto the protein, RNA aptamers, and ribozymes against the protein.

A “B-cell antagonist” is a molecule that, upon binding to a B-cellsurface marker, destroys or depletes B cells in a mammal and/orinterferes with one or more B-cell functions, e.g. by reducing orpreventing a humoral response elicited by the B cell. The antagonist incertain instances is able to deplete B cells (i.e. reduce circulatingB-cell levels) in a mammal treated therewith. Such depletion may beachieved via various mechanisms such as ADCC and/or CDC, inhibition ofB-cell proliferation, and/or induction of B-cell death (e.g. viaapoptosis). Exemplary antagonists include synthetic or native-sequencepeptides, fusion proteins, and small-molecule antagonists that bind tothe B-cell marker, optionally conjugated with or fused to a cytotoxicagent. Examples include but are not limited to, e.g., CD22 antibodies,CD20 antibodies, BR3 antibodies (e.g., WO0224909), and BR3-Fcimmunoadhesin.

Examples of CD20 antibodies include: “C2B8,” which is now called“rituximab” (“RITUXAN®”) (U.S. Pat. No. 5,736,137); theyttrium-[90]-labeled 2B8 murine antibody designated “Y2B8” or“ibritumomab tiuxetan” (ZEVALIN®) commercially available from IDECPharmaceuticals, Inc. (U.S. Pat. No. 5,736,137; 2B8 deposited with ATCCunder accession no. HB11388 on Jun. 22, 1993); murine IgG2a “B1,” alsocalled “tositumomab,” optionally labeled with ¹³¹I to generate the“¹³¹I-B1” or “iodine I¹³¹ tositumomab” antibody (BEXXAR™) commerciallyavailable from Corixa (see, also, U.S. Pat. No. 5,595,721); murinemonoclonal antibody “1F5” (Press et al. Blood 69(2):584-591 (1987) andvariants thereof including “framework-patched” or humanized 1F5 (WO2003/002607, Leung, S.; ATCC deposit HB-96450); murine 2H7 and chimeric2H7 antibody (U.S. Pat. No. 5,677,180); humanized 2H7 (see, e.g.,WO04/056312; US20060024295); HUMAX-CD20™ antibodies (Genmab, Denmark);the human monoclonal antibodies set forth in WO 2004/035607 (Teeling etal.); AME-133™ antibodies (Applied Molecular Evolution); A20 antibody orvariants thereof such as chimeric or humanized A20 antibody (cA20, hA20,respectively) (US 2003/0219433, Immunomedics); and monoclonal antibodiesL27, G28-2, 93-1 B3, B-C1 or NU-B2 available from the InternationalLeukocyte Typing Workshop (Valentine et al., In: Leukocyte Typing III(McMichael, Ed., p. 440, Oxford University Press (1987)).

The terms “BAFF,” “BAFF polypeptide,” “TALL-1” or “TALL-1 polypeptide,”“BLyS”, and “THANK” when used herein encompass “native-sequence BAFFpolypeptides” and “BAFF variants.” “BAFF” is a designation given tothose polypeptides that have the human BAFF sequence as set forth in,for example, U.S. Pat. Pub. No. 2006/0110387, and homologs and fragmentsand variants thereof, which have the biological activity of thenative-sequence BAFF. A biological activity of BAFF can be selected fromthe group consisting of promoting B-cell survival, promoting B-cellmaturation, and binding to BR3. The term “BAFF” includes thosepolypeptides described in Shu et al., J. Leukocyte Biol., 65:680 (1999);GenBank Accession No. AF136293; WO 1998/18921; EP 869,180; WO1998/27114; WO 1999/12964; WO 1999/33980; Moore et al., Science,285:260-263 (1999); Schneider et al., J. Exp. Med., 189:1747-1756(1999); and Mukhopadhyay et al., J. Biol. Chem., 274:15978-15981 (1999).

The term “BAFF, antagonist” as used herein is used in the broadestsense, and includes any molecule that (1) binds a native-sequence BAFFpolypeptide or binds a native-sequence BR3 polypeptide to block,partially or fully, BR3 interaction with BAFF polypeptide, and (2)partially or fully blocks, inhibits, or neutralizes native-sequence BAFFsignaling. Native-sequence BAFF polypeptide signaling promotes, amongother things, B-cell survival and B-cell maturation. The inhibition,blockage, or neutralization of BAFF signaling results in, inter alia, areduction in the number of B cells. A BAFF antagonist as defined hereinwill partially or fully block, inhibit, or neutralize one or morebiological activities of a BAFF polypeptide, in vitro or in vivo. In oneembodiment, a biologically active BAFF potentiates any one or acombination of the following events in vitro or in vivo: an increasedsurvival of B cells, an increased level of IgG and/or IgM, an increasednumbers of plasma cells, and processing of NF-κb2/100 to p52 NF-κβ insplenic B cells (e.g., Batten et al., J. Exp. Med. 192:1453-1465 (2000);Moore et al., Science 285:260-263 (1999); and Kayagaki et al., Immunity,10:515-524 (2002)).

In some embodiments, a BAFF antagonist as defined herein includesanti-BAFF antibodies, BAFF-binding polypeptides (includingimmunoadhesins and peptides), and BAFF-binding small molecules. BAFFantagonists include, for example, the BAFF-binding antibodies describedin WO 2002/02641 (e.g., antibodies comprising the amino acid sequence ofany of SEQ ID NOS:1-46, 321-329, 834-872, 1563-1595, 1881-1905 of Table1 thereof). In a further embodiment, the immunoadhesin comprises aBAFF-binding region of a BAFF receptor (e.g., an extracellular domain ofBR3, BCMA, or TACI). In a still further embodiment, the immunoadhesin isBR3-Fc. Other examples of BAFF-binding Fc proteins can be found in WO2002/66516, WO 2000/40716, WO 2001/87979, WO 2003/024991, WO 2002/16412,WO 2002/38766, WO 2002/092620, and WO 2001/12812. Methods of making BAFFantagonists are described, for example, in US 2005/0095243 and US2005/0163775.

The terms “BR3”, “BR3 polypeptide” or “BR3 receptor” when used hereinencompass native-sequence BR3 polypeptides and BR3 variants, as definedhereinbelow. “BR3” is a designation given to those polypeptidescomprising, for example, the human BR3 sequence set forth in WO2003/14294 and US 2005/0070689. BR3 polypeptides can be isolated from avariety of sources, such as from human tissue types or from anothersource, or prepared by recombinant and/or synthetic methods. The termBR3 includes the BR3 polypeptides described in WO 2002/24909, WO2003/14294, and US 2005/0070689. Anti-BR3 antibodies can be prepared inaccordance with methods set for in, for example, WO 2003/14294 and US2005/0070689.

A “native-sequence” BR3 polypeptide or “native BR3” comprises apolypeptide having the same amino acid sequence as the corresponding BR3polypeptide derived from nature. Such native-sequence BR3 polypeptidescan be isolated from nature or can be produced by recombinant and/orsynthetic means. The term “native-sequence BR3 polypeptide” specificallyencompasses naturally occurring truncated, soluble or secreted forms(e.g., an extracellular domain sequence), naturally occurring variantforms (e.g., alternatively spliced forms) and naturally occurringallelic variants of the polypeptide. The BR3 polypeptides of theinvention include the BR3 polypeptide comprising or consisting of thecontiguous sequence of amino acid residues 1 to 184 of a human BR3 (seeWO 2003/14294 and US 2005/0070689).

A BR3 “extracellular domain” or “ECD” refers to a form of the BR3polypeptide that is essentially free of the transmembrane andcytoplasmic domains. ECD forms of BR3 include a polypeptide comprisingany one of the amino acid sequences selected from the group consistingof amino acids 1-77, 2-62, 2-71, 1-61, 7-71, 23-38 and 2-63 of humanBR3. In certain embodiments, BAFF antagonists are polypeptidescomprising any one of the above-mentioned ECD forms of human BR3 andvariants and fragments thereof that bind a native BAFF.

“BR3 variant” means a BR3 polypeptide having at least about 80% aminoacid sequence identity with the amino acid sequence of anative-sequence, full-length BR3 or BR3 ECD and binds a native-sequenceBAFF polypeptide. Optionally, the BR3 variant includes a singlecysteine-rich domain. Such BR3 variant polypeptides include, forinstance, BR3 polypeptides wherein one or more amino acid residues areadded, or deleted, at the N- and/or C-terminus, as well as within one ormore internal domains, of the full-length amino acid sequence. Fragmentsof the BR3ECD that bind a native sequence BAFF polypeptide are alsocontemplated.

The term “APRIL antagonist” as used herein is used in the broadestsense, and includes any molecule that (1) binds a native-sequence APRILpolypeptide or binds a native-sequence ligand to APRIL to block,partially or fully, the ligand's interaction with APRIL polypeptide, and(2) partially or fully blocks, inhibits, or neutralizes native-sequenceAPRIL signaling. Native-sequence APRIL polypeptide signaling promotes,among other things, B-cell survival and B-cell maturation. APRIL (aproliferation-inducing ligand) is a TNF family member with a sharedreceptor to BAFF. Examples of APRIL antagonists include but are notlimited to atacicept (same as TACI-Ig immunoadhesin) and a BAFF/APRILantagonist (soluble BCMA-Fc).

The term “cytokine” is a generic term for proteins released by one cellpopulation that act on another cell as intercellular mediators. Examplesof such cytokines are lymphokines, monokines; interleukins (ILs) such asIL-1, IL-1a, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-11,IL-12, IL-15, IL-17A, IL-17F, IL-17A/F; a tumor necrosis factor such asTNF-α or TNF-β; and other polypeptide factors including LIF and kitligand (KL). As used herein, the term cytokine includes proteins fromnatural sources or from recombinant cell culture and biologically activeequivalents of the native-sequence cytokines, including syntheticallyproduced small-molecule entities and pharmaceutically acceptablederivatives and salts thereof.

As used herein, “tumor necrosis factor-alpha (TNF-alpha)” refers to ahuman TNF-alpha molecule comprising the amino acid sequence as describedin Pennica et al., Nature, 312:721 (1984) or Aggarwal et al., JBC,260:2345 (1985).

A “TNF-alpha inhibitor” herein is an agent that inhibits, to someextent, a biological function of TNF-alpha, generally through binding toTNF-alpha and neutralizing its activity. Examples of TNF-alphainhibitors specifically contemplated herein are etanercept (ENBREL®),infliximab (REMICADE®), adalimumab (HUMIRA®), golimumab (SIMPONI™), andcertolizumab pegol (CIMZIA®).

Examples of “disease-modifying anti-rheumatic drugs” or “DMARDs” includehydroxycloroquine, sulfasalazine, methotrexate (plus oral andsubcutaneous methrotrexate), leflunomide, azathioprine, D-penicillamine,Gold (oral), Gold (intramuscular), minocycline, cyclosporine,Staphylococcal protein A immunoadsorption, including salts andderivatives thereof, etc.

“CTLA4” is expressed on activated T lymphocytes and is involved indown-regulation of the immune response. Other names for CTLA4 in theliterature include cytotoxic T-lymphocyte-associated antigen 4,cytotoxic T-lymphocyte-associated protein 4, cell differentiationantigen CD 152, and cytotoxic T-lymphocyte-associated granule serineprotease 4.

A therapeutic agent that has “marketing approval,” or that has been“approved as a therapeutic agent,” or grammatical variations thereof ofthese phrases, as used herein, refer to an agent (e.g., in the form of adrug formulation, medicament) that is approved, licensed, registered orauthorized by a relevant governmental entity (e.g., federal, state orlocal regulatory agency, department, bureau) to be sold by and/orthrough and/or on behalf of a commercial entity (e.g., a for-profitentity) for the treatment of a particular disorder (e.g., RA) or apatient subpopulation (e.g., patients of a particular ethnicity, gender,lifestyle, disease risk profile, etc.). A relevant governmental entityincludes, for example, the Food and Drug Administration (FDA), EuropeanMedicines Agency (EMA), and equivalents thereof.

“Antibodies” (Abs) and “immunoglobulins” (Igs) refer to glycoproteinshaving similar structural characteristics. While antibodies exhibitbinding specificity to a specific antigen, immunoglobulins include bothantibodies and other antibody-like molecules which generally lackantigen specificity. Polypeptides of the latter kind are, for example,produced at low levels by the lymph system and at increased levels bymyelomas.

The terms “antibody” and “immunoglobulin” are used interchangeably inthe broadest sense and include monoclonal antibodies (e.g., full lengthor intact monoclonal antibodies), polyclonal antibodies, monovalentantibodies, multivalent antibodies, multispecific antibodies (e.g.,bispecific antibodies so long as they exhibit the desired biologicalactivity) and may also include certain antibody fragments (as describedin greater detail herein). An antibody can be chimeric, human, humanizedand/or affinity matured.

The terms “full length antibody,” “intact antibody” and “whole antibody”are used herein interchangeably to refer to an antibody in itssubstantially intact form, not antibody fragments as defined below. Theterms particularly refer to an antibody with heavy chains that containthe Fc region.

“Antibody fragments” comprise a portion of an intact antibody,preferably comprising the antigen binding region thereof. Examples ofantibody fragments include Fab, Fab′, F(ab′)₂, and Fv fragments;diabodies; linear antibodies; single-chain antibody molecules; andmultispecific antibodies formed from antibody fragments.

Papain digestion of antibodies produces two identical antigen-bindingfragments, called “Fab” fragments, each with a single antigen-bindingsite, and a residual “Fc” fragment, whose name reflects its ability tocrystallize readily. Pepsin treatment yields an F(ab′)₂ fragment thathas two antigen-combining sites and is still capable of cross-linkingantigen.

“Fv” is a minimum antibody fragment which contains a completeantigen-binding site. In one embodiment, a two-chain Fv species consistsof a dimer of one heavy- and one light-chain variable domain in tight,non-covalent association. Collectively, the six CDRs of an Fv conferantigen-binding specificity to the antibody. However, even a singlevariable domain (or half of an Fv comprising only three CDRs specificfor an antigen) has the ability to recognize and bind antigen, althoughat a lower affinity than the entire binding site.

The Fab fragment contains the heavy- and light-chain variable domainsand also contains the constant domain of the light chain and the firstconstant domain (CH1) of the heavy chain. Fab′ fragments differ from Fabfragments by the addition of a few residues at the carboxy terminus ofthe heavy chain CH1 domain including one or more cysteines from theantibody hinge region. Fab′-SH is the designation herein for Fab′ inwhich the cysteine residue(s) of the constant domains bear a free thiolgroup. F(ab′)₂ antibody fragments originally were produced as pairs ofFab′ fragments which have hinge cysteines between them. Other chemicalcouplings of antibody fragments are also known.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies comprising the population are identicalexcept for possible mutations, e.g., naturally occurring mutations, thatmay be present in minor amounts. Thus, the modifier “monoclonal”indicates the character of the antibody as not being a mixture ofdiscrete antibodies. In certain embodiments, such a monoclonal antibodytypically includes an antibody comprising a polypeptide sequence thatbinds a target, wherein the target-binding polypeptide sequence wasobtained by a process that includes the selection of a single targetbinding polypeptide sequence from a plurality of polypeptide sequences.For example, the selection process can be the selection of a uniqueclone from a plurality of clones, such as a pool of hybridoma clones,phage clones, or recombinant DNA clones. It should be understood that aselected target binding sequence can be further altered, for example, toimprove affinity for the target, to humanize the target bindingsequence, to improve its production in cell culture, to reduce itsimmunogenicity in vivo, to create a multispecific antibody, etc., andthat an antibody comprising the altered target binding sequence is alsoa monoclonal antibody of this invention. In contrast to polyclonalantibody preparations which typically include different antibodiesdirected against different determinants (epitopes), each monoclonalantibody of a monoclonal antibody preparation is directed against asingle determinant on an antigen. In addition to their specificity,monoclonal antibody preparations are advantageous in that they aretypically uncontaminated by other immunoglobulins.

The modifier “monoclonal” indicates the character of the antibody asbeing obtained from a substantially homogeneous population ofantibodies, and is not to be construed as requiring production of theantibody by any particular method. For example, the monoclonalantibodies to be used in accordance with the present invention may bemade by a variety of techniques, including, for example, the hybridomamethod (e.g., Kohler et al., Nature, 256: 495 (1975); Harlow et al.,Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press,2^(nd) ed. 1988); Hammerling et al., in: Monoclonal Antibodies andT-Cell Hybridomas 563-681 (Elsevier, N.Y., 1981)), recombinant DNAmethods (see, e.g., U.S. Pat. No. 4,816,567), phage display technologies(see, e.g., Clackson et al., Nature, 352: 624-628 (1991); Marks et al.,J. Mol. Biol. 222: 581-597 (1992); Sidhu et al., J. Mol. Biol. 338(2):299-310 (2004); Lee et al., J. Mol. Biol. 340(5): 1073-1093 (2004);Fellouse, Proc. Natl. Acad. Sci. USA 101(34): 12467-12472 (2004); andLee et al., J. Immunol. Methods 284(1-2): 119-132 (2004), andtechnologies for producing human or human-like antibodies in animalsthat have parts or all of the human immunoglobulin loci or genesencoding human immunoglobulin sequences (see, e.g., WO98/24893;WO96/34096; WO96/33735; WO91/10741; Jakobovits et al., Proc. Natl. Acad.Sci. USA 90: 2551 (1993); Jakobovits et al., Nature 362: 255-258 (1993);Bruggemann et al., Year in Immunol. 7:33 (1993); U.S. Pat. Nos.5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016; Markset al., Bio. Technology 10: 779-783 (1992); Lonberg et al., Nature 368:856-859 (1994); Morrison, Nature 368: 812-813 (1994); Fishwild et al.,Nature Biotechnol. 14: 845-851 (1996); Neuberger, Nature Biotechnol. 14:826 (1996) and Lonberg and Huszar, Intern. Rev. Immunol. 13: 65-93(1995).

The monoclonal antibodies herein specifically include “chimeric”antibodies in which a portion of the heavy and/or light chain isidentical with or homologous to corresponding sequences in antibodiesderived from a particular species or belonging to a particular antibodyclass or subclass, while the remainder of the chain(s) is identical withor homologous to corresponding sequences in antibodies derived fromanother species or belonging to another antibody class or subclass, aswell as fragments of such antibodies, so long as they exhibit thedesired biological activity (U.S. Pat. No. 4,816,567; and Morrison etal., Proc. Natl. Acad. Sci. USA 81:6855-9855 (1984)).

“Humanized” forms of non-human (e.g., murine) antibodies are chimericantibodies that contain minimal sequence derived from non-humanimmunoglobulin. In one embodiment, a humanized antibody is a humanimmunoglobulin (recipient antibody) in which residues from ahypervariable region of the recipient are replaced by residues from ahypervariable region of a non-human species (donor antibody) such asmouse, rat, rabbit, or nonhuman primate having the desired specificity,affinity, and/or capacity. In some instances, framework region (FR)residues of the human immunoglobulin are replaced by correspondingnon-human residues. Furthermore, humanized antibodies may compriseresidues that are not found in the recipient antibody or in the donorantibody. These modifications may be made to further refine antibodyperformance. In general, a humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the hypervariable loops correspondto those of a non-human immunoglobulin, and all or substantially all ofthe FRs are those of a human immunoglobulin sequence. The humanizedantibody optionally will also comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin. For further details, see Jones et al., Nature321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); andPresta, Curr. Op. Struct. Biol. 2:593-596 (1992). See also the followingreview articles and references cited therein: Vaswani and Hamilton, Ann.Allergy, Asthma & Immunol. 1:105-115 (1998); Harris, Biochem. Soc.Transactions 23:1035-1038 (1995); Hurle and Gross, Curr. Op. Biotech.5:428-433 (1994).

A “human antibody” is one which comprises an amino acid sequencecorresponding to that of an antibody produced by a human and/or has beenmade using any of the techniques for making human antibodies asdisclosed herein. Such techniques include screening human-derivedcombinatorial libraries, such as phage display libraries (see, e.g.,Marks et al., J. Mol. Biol., 222: 581-597 (1991) and Hoogenboom et al.,Nucl. Acids Res., 19: 4133-4137 (1991)); using human myeloma andmouse-human heteromyeloma cell lines for the production of humanmonoclonal antibodies (see, e.g., Kozbor J. Immunol., 133: 3001 (1984);Brodeur et al., Monoclonal Antibody Production Techniques andApplications, pp. 55-93 (Marcel Dekker, Inc., New York, 1987); andBoerner et al., J. Immunol., 147: 86 (1991)); and generating monoclonalantibodies in transgenic animals (e.g., mice) that are capable ofproducing a full repertoire of human antibodies in the absence ofendogenous immunoglobulin production (see, e.g., Jakobovits et al.,Proc. Natl. Acad. Sci. USA, 90: 2551 (1993); Jakobovits et al., Nature,362: 255 (1993); Bruggermann et al., Year in Immunol., 7: 33 (1993)).This definition of a human antibody specifically excludes a humanizedantibody comprising antigen-binding residues from a non-human animal.

An “affinity matured” antibody is one with one or more alterations inone or more CDRs thereof which result in an improvement in the affinityof the antibody for antigen, compared to a parent antibody which doesnot possess those alteration(s). In one embodiment, an affinity maturedantibody has nanomolar or even picomolar affinities for the targetantigen. Affinity matured antibodies are produced by procedures known inthe art. Marks et al. Bio/Technology 10:779-783 (1992) describesaffinity maturation by VH and VL domain shuffling. Random mutagenesis ofHVR and/or framework residues is described by: Barbas et al. Proc Nat.Acad. Sci. USA 91:3809-3813 (1994); Schier et al. Gene 169:147-155(1995); Yelton et al. J. Immunol. 155:1994-2004 (1995); Jackson et al.,J. Immunol. 154(7):3310-9 (1995); and Hawkins et al, J. Mol. Biol.226:889-896 (1992).

A “blocking antibody” or an “antagonist antibody” is one which inhibitsor reduces a biological activity of the antigen it binds. Certainblocking antibodies or antagonist antibodies partially or completelyinhibit the biological activity of the antigen.

As used herein, “growth-inhibitory” antibodies are those that prevent orreduce proliferation of a cell expressing an antigen to which theantibody binds. For example, the antibody may prevent or reduceproliferation of B cells in vitro and/or in vivo.

Antibodies that “induce apoptosis” refer to antibodies that induceprogrammed cell death, e.g. of a B cell, as determined by standardapoptosis assays, such as binding of annexin V, fragmentation of DNA,cell shrinkage, dilation of endoplasmic reticulum, cell fragmentation,and/or formation of membrane vesicles (called apoptotic bodies).

Antibody “effector functions” refer to those biological activitiesattributable to the Fc region (a native-sequence Fc region oramino-acid-sequence-variant Fc region) of an antibody, and vary with theantibody isotype. Examples of antibody effector functions include butare not limited to: C1q binding and complement-dependent cytotoxicity(CDC); Fc-receptor binding; antibody-dependent cell-mediatedcytotoxicity (ADCC); phagocytosis; down-regulation of cell-surfacereceptors (e.g. B-cell receptor); and B-cell activation.

The term “Fc region” herein is used to define a C-terminal region of animmunoglobulin heavy chain, including native-sequence Fc regions andvariant Fc regions. Although the boundaries of the Fc region of animmunoglobulin heavy chain might vary, the human IgG heavy-chain Fcregion is typically defined to stretch from an amino acid residue atposition Cys226, or from Pro230, to the carboxyl-terminus thereof. TheC-terminal lysine (residue 447 according to the EU numbering system) ofthe Fc region may be removed, for example, during production orpurification of the antibody, or by recombinantly engineering thenucleic acid encoding a heavy chain of the antibody. Accordingly, acomposition of intact antibodies may comprise antibody populations withall K447 residues removed, antibody populations with no K447 residuesremoved, and antibody populations having a mixture of antibodies withand without the K447 residue.

Unless indicated otherwise herein, the numbering of the residues in animmunoglobulin heavy chain is that of the EU index as in Kabat (Kabat etal., Sequences of Proteins of Immunological Interest, Ed. 5 (PublicHealth Service, National Institutes of Health, Bethesda, Md., 1991)).The “EU index as in Kabat” refers to the residue numbering of the humanIgG1 EU antibody.

A “functional Fc region” possesses an “effector function” of anative-sequence Fc region. Exemplary “effector functions” include butare not limited to C1q binding; CDC; Fc-receptor binding; ADCC;phagocytosis; down-regulation of cell-surface receptors (e.g. B-cellreceptor; BCR), etc. Such effector functions generally require the Fcregion to be combined with a binding domain (e.g. an antibody-variabledomain) and can be assessed using various assays as disclosed, forexample, herein.

A “native-sequence Fc region” comprises an amino acid sequence identicalto the amino acid sequence of an Fc region found in nature.Native-sequence human Fc regions include a native-sequence human IgG1 Fcregion (non-A and A allotypes); native-sequence human IgG2 Fc region;native-sequence human IgG3 Fc region; and native-sequence human IgG4 Fcregion, as well as naturally occurring variants thereof.

A “variant Fc region” comprises an amino acid sequence which differsfrom that of a native-sequence Fc region by virtue of at least one aminoacid modification, typically one or more amino acid substitution(s).

The term “Fc-region-comprising antibody” refers to an antibody thatcomprises an Fc region. The C-terminal lysine (residue 447 according tothe EU numbering system) of the Fc region may be removed, for example,during purification of the antibody or by recombinant engineering thenucleic acid encoding the antibody. Accordingly, a compositioncomprising an antibody having an Fc region can comprise an antibody withK447, with all K447 removed, or a mixture of antibodies with and withoutthe K447 residue. “Fc receptor” or “FcR” describes a receptor that bindsto the Fc region of an antibody. In some embodiments, an FcR is anative-human FcR. In some embodiments, an FcR is one which binds an IgGantibody (a gamma receptor) and includes receptors of the FcγRI, FcγRII,and FcγRIII subclasses, including allelic variants and alternativelyspliced forms of those receptors. FcγRII receptors include FcγRIIA (an“activating receptor”) and FcγRIIB (an “inhibiting receptor”), whichhave similar amino acid sequences that differ primarily in thecytoplasmic domains thereof. Activating receptor FcγRIIA contains animmunoreceptor tyrosine-based activation motif (ITAM) in its cytoplasmicdomain. Inhibiting receptor FcγRIIB contains an immunoreceptortyrosine-based inhibition motif (ITIM) in its cytoplasmic domain. (see,e.g., Daëron, Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed,for example, in Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991);Capel et al., Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab.Clin. Med. 126:330-41 (1995). Other FcRs, including those to beidentified in the future, are encompassed by the term “FcR” herein.

The term “Fc receptor” or “FcR” also includes the neonatal receptor,FcRn, which is responsible for the transfer of maternal IgGs to thefetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al., J.Immunol. 24:249 (1994)) and regulation of homeostasis ofimmunoglobulins. Methods of measuring binding to FcRn are known (see,e.g., Ghetie and Ward, Immunology Today, 18 (12):592-8 (1997); Ghetie etal., Nature Biotechnology, 15 (7):637-40 (1997); Hinton et al., J. Biol.Chem., 279(8):6213-6 (2004); WO 2004/92219 (Hinton et al.).

Binding to human FcRn in vivo and serum half-life of human FcRnhigh-affinity binding polypeptides can be assayed, e.g., in transgenicmice or transfected human cell lines expressing human FcRn, or inprimates to which the polypeptides with a variant Fc region areadministered. WO 2000/42072 (Presta) describes antibody variants withimproved or diminished binding to FcRs. See, also, for example, Shieldset al., J. Biol. Chem., 9(2): 6591-6604 (2001). “Human effector cells”are leukocytes which express one or more FcRs and perform effectorfunctions. In certain embodiments, the cells express at least FcγRIIIand perform ADCC effector function(s). Examples of human leukocyteswhich mediate ADCC include peripheral blood mononuclear cells (PBMC),natural-killer (NK) cells, monocytes, cytotoxic T cells, andneutrophils. The effector cells may be isolated from a native source,e.g., from blood.

“Antibody-dependent cell-mediated cytotoxicity” or “ADCC” refers to aform of cytotoxicity in which secreted Ig bound onto Fc receptors (FcRs)present on certain cytotoxic cells (e.g., NK cells, neutrophils, andmacrophages) enables these cytotoxic effector cells to bind specificallyto an antigen-bearing target cell and subsequently kill the target cellwith cytotoxins. The primary cells for mediating ADCC, NK cells, expressFcγRIII only, whereas monocytes express FcγRI, FcγRII, and FcγRIII. FcRexpression on hematopoietic cells is summarized in Table 3 on page 464of Ravetch and Kinet, Annu. Rev. Immunol., 9:457-492 (1991). To assessADCC activity of a molecule of interest, an in vitro ADCC assay, such asthat described in U.S. Pat. No. 5,500,362 or 5,821,337 or U.S. Pat. No.6,737,056 (Presta), may be performed. Useful effector cells for suchassays include PBMC and NK cells. Alternatively, or additionally, ADCCactivity of the molecule of interest may be assessed in vivo, e.g., inan animal model such as that disclosed in Clynes et al., Proc. Natl.Acad. Sci. (USA), 95:652-656 (1998).

“Complement-dependent cytotoxicity” or “CDC” refers to the lysis of atarget cell in the presence of complement. Activation of the classicalcomplement pathway is initiated by the binding of the first component ofthe complement system (C1q) to antibodies (of the appropriate subclass),which are bound to their cognate antigen. To assess complementactivation, a CDC assay, e.g. as described in Gazzano-Santoro et al., J.Immunol. Methods, 202:163 (1996), may be performed. Polypeptide variantswith altered Fc region amino acid sequences (polypeptides with a variantFc region) and increased or decreased C1q binding capability aredescribed, e.g., in U.S. Pat. No. 6,194,551 and WO 1999/51642. See,also, e.g., Idusogie et al., J. Immunol. 164:4178-4184 (2000).

“Binding affinity” generally refers to the strength of the sum total ofnoncovalent interactions between a single binding site of a molecule(e.g., an antibody) and its binding partner (e.g., an antigen). Unlessindicated otherwise, as used herein, “binding affinity” refers tointrinsic binding affinity which reflects a 1:1 interaction betweenmembers of a binding pair (e.g., antibody and antigen). The affinity ofa molecule X for its partner Y can generally be represented by thedissociation constant (Kd). Affinity can be measured by common methodsknown in the art, including those described herein. Low-affinityantibodies generally bind antigen slowly and tend to dissociate readily,whereas high-affinity antibodies generally bind antigen faster and tendto remain bound longer. A variety of methods of measuring bindingaffinity are known in the art.

The term “substantially similar” or “substantially the same,” as usedherein, denotes a sufficiently high degree of similarity between twonumeric values (for example, one associated with an antibody of theinvention and the other associated with a reference/comparatorantibody), such that one of skill in the art would consider thedifference between the two values to be of little or no biologicaland/or statistical significance within the context of the biologicalcharacteristic measured by said values (e.g., Kd values). The differencebetween said two values is, for example, less than about 50%, less thanabout 40%, less than about 30%, less than about 20%, and/or less thanabout 10% as a function of the reference/comparator value.

The phrase “substantially reduced,” or “substantially different,” asused herein, denotes a sufficiently high degree of difference betweentwo numeric values (generally one associated with a molecule and theother associated with a reference/comparator molecule) such that one ofskill in the art would consider the difference between the two values tobe of statistical significance within the context of the biologicalcharacteristic measured by said values (e.g., Kd values). The differencebetween said two values is, for example, greater than about 10%, greaterthan about 20%, greater than about 30%, greater than about 40%, and/orgreater than about 50% as a function of the value for thereference/comparator molecule.

The word “label” when used herein refers to a detectable compound orcomposition. The label is typically conjugated or fused directly orindirectly to a reagent, such as a nucleic acid probe or an antibody,and facilitates detection of the reagent to which it is conjugated orfused. The label may itself be detectable (e.g., radioisotope labels orfluorescent labels) or, in the case of an enzymatic label, may catalyzechemical alteration of a substrate compound or composition which resultsin a detectable product.

An “isolated” biological molecule, such as a nucleic acid, polypeptide,or antibody, is one which has been identified and separated and/orrecovered from at least one component of its natural environment.

Reference to “about” a value or parameter herein includes (anddescribes) embodiments that are directed to that value or parameter perse. For example, description referring to “about X” includes descriptionof “X.”

The term “pharmaceutical formulation” refers to a sterile preparationthat is in such form as to permit the biological activity of themedicament to be effective, and which contains no additional componentsthat are unacceptably toxic to a subject to which the formulation wouldbe administered.

A “sterile” formulation is aseptic or free from all livingmicroorganisms and their spores.

A “package insert” is used to refer to instructions customarily includedin commercial packages of therapeutic products or medicaments, thatcontain information about the indications, usage, dosage,administration, contraindications, other therapeutic products to becombined with the packaged product, and/or warnings concerning the useof such therapeutic products or medicaments and the like.

A “kit” is any manufacture (e.g a package or container) comprising atleast one reagent, e.g., a medicament for treatment of RA or jointdamage, or a probe for specifically detecting a biomarker gene orprotein of the invention. In certain embodiments, the manufacture ispromoted, distributed, or sold as a unit for performing the methods ofthe present invention.

A “target audience” is a group of people or an institution to whom or towhich a particular medicament is being promoted or intended to bepromoted, as by marketing or advertising, especially for particularuses, treatments, or indications, such as individual patients, patientpopulations, readers of newspapers, medical literature, and magazines,television or internet viewers, radio or internet listeners, physicians,drug companies, etc.

The term “serum sample” refers to any serum sample obtained from anindividual. Methods for obtaining sera from mammals are well known inthe art.

The term “whole blood” refers to any whole blood sample obtained from anindividual. Typically, whole blood contains all of the blood components,e.g., cellular components and plasma. Methods for obtaining whole bloodfrom mammals are well known in the art.

The expression “not responsive to,” “non-response” and grammaticalvariants thereof, as it relates to the reaction of subjects or patientsto one or more of the medicaments (therapeutic agents) that werepreviously administered to them, describes those subjects or patientswho, upon administration of such medicament(s), did not exhibit any oradequate signs of treatment of the disorder for which they were beingtreated, or they exhibited a clinically unacceptably high degree oftoxicity to the medicament(s), or they did not maintain the signs oftreatment after first being administered such medicament(s), with theword treatment being used in this context as defined herein. The phrase“not responsive” includes a description of those subjects who areresistant and/or refractory to the previously administeredmedication(s), and includes the situations in which a subject or patienthas progressed while receiving the medicament(s) that he or she is beinggiven, and in which a subject or patient has progressed within 12 months(for example, within six months) after completing a regimen involvingthe medicament(s) to which he or she is no longer responsive. Thenon-responsiveness to one or more medicaments thus includes subjects whocontinue to have active disease following previous or current treatmenttherewith. For instance, a patient may have active disease activityafter about one to three months, or three to six months, or six to 12months, of therapy with the medicament(s) to which they arenon-responsive. Such responsiveness may be assessed by a clinicianskilled in treating the disorder in question.

For purposes of non-response to medicament(s), a subject who experiences“a clinically unacceptably high level of toxicity” from previous orcurrent treatment with one or more medicaments experiences one or morenegative side-effects or adverse events associated therewith that areconsidered by an experienced clinician to be significant, such as, forexample, serious infections, congestive heart failure, demyelination(leading to multiple sclerosis), significant hypersensitivity,neuropathological events, high degrees of autoimmunity, a cancer such asendometrial cancer, non-Hodgkin's lymphoma, breast cancer, prostatecancer, lung cancer, ovarian cancer, or melanoma, tuberculosis (TB), andthe like.

The “amount” or “level” of a biomarker associated with an increasedclinical benefit to a patient suffering from a certain disease ordisorder, or predictive of response to a particular therapeutic agent ortreatment regimen, is a detectable level in a biological sample. Thesecan be measured by methods known to one skilled in the art and alsodisclosed herein. The expression level or amount of biomarker assessedcan be used to determine the response or the predicted response to atreatment or therapeutic agent.

The terms “level of expression” or “expression level” in general areused interchangeably and generally refer to the amount of apolynucleotide or an amino acid product or protein in a biologicalsample. “Expression” generally refers to the process by whichgene-encoded information is converted into the structures present andoperating in the cell. Therefore, as used herein, “expression” of a genemay refer to transcription into a polynucleotide, translation into aprotein, or even posttranslational modification of the protein.Fragments of the transcribed polynucleotide, the translated protein, orthe post-translationally modified protein shall also be regarded asexpressed whether they originate from a transcript generated byalternative splicing or a degraded transcript, or from apost-translational processing of the protein, e.g., by proteolysis.“Expressed genes” include those that are transcribed into apolynucleotide as mRNA and then translated into a protein, and alsothose that are transcribed into RNA but not translated into a protein(for example, transfer and ribosomal RNAs).

Autoimmune Diseases

Autoimmune diseases remain clinically important diseases in humans. Asthe name implies, autoimmune diseases act through the body's own immunesystem. While the pathological mechanisms differ among individual typesof autoimmune diseases, one general mechanism involves the generation ofantibodies (referred to herein as self-reactive antibodies orautoantibodies) directed against specific endogenous proteins.Physicians and scientists have identified more than 70 clinicallydistinct autoimmune diseases, including RA, multiple sclerosis (MS),vasculitis, immune-mediated diabetes, and lupus such as systemic lupuserythematosus (SLE). While many autoimmune diseases are rare—affectingfewer than 200,000 individuals—collectively, these diseases afflictmillions of Americans, an estimated five percent of the population, withwomen disproportionately affected by most diseases. The chronic natureof these diseases leads to an immense social and financial burden.

Inflammatory arthritis is a prominent clinical manifestation in diverseautoimmune disorders including RA, psoriatic arthritis (PsA), SLE,Sjögren's syndrome, and polymyositis. Most of these patients developjoint deformities on physical examination but typically only RA and PsApatients manifest bone erosions on imaging studies.

Rheumatoid Arthritis

RA is a chronic inflammatory disease that affects approximately 0.5 to1% of the adult population in northern Europe and North America, and aslightly lower proportion in other parts of the world. Alamanos andDrosos, Autoimmun. Rev., 4: 130-136 (2005). It is a systemicinflammatory disease characterized by chronic inflammation in thesynovial membrane of affected joints, which ultimately leads to loss ofdaily function due to chronic pain and fatigue. The majority of patientsalso experience progressive deterioration of cartilage and bone in theaffected joints, which may eventually lead to permanent disability. Thelong-term prognosis of RA is poor, with approximately 50% of patientsexperiencing significant functional disability within 10 years from thetime of diagnosis. Keystone, Rheumatology, 44 (Suppl. 2): ii8-ii12(2005). Life expectancy is reduced by an average of 3-10 years. Alamanosand Drosos, supra. Patients with a high titer of rheumatoid factor (RF)(approximately 80% of patients) have more aggressive disease (Bukhari etal., Arthritis Rheum., 46: 906-912 (2002)), with a worse long-termoutcome and increased mortality over those who are RF negative.Heliovaara et al., Ann. Rheum. Dis., 54: 811-814 (1995)).

The pathogenesis of chronic inflammatory bone diseases, such as RA, isnot fully elucidated. Such diseases are accompanied by bone loss aroundaffected joints due to increased osteoclastic resorption. This processis mediated largely by increased local production of pro-inflammatorycytokines. Teitelbaum, Science, 289:1504-1508 (2000); Goldring andGravallese, Arthritis Res., 2(1):33-37 (2000). These cytokines can actdirectly on cells in the osteoclast lineage or indirectly by affectingthe production of the essential osteoclast differentiation factor,receptor activator of NFκB ligand (RANKL), and/or its soluble decoyreceptor, osteoprotegerin (OPG), by osteoblast/stromal cells. Hossbaueret al., J. Bone Min. Res., 15(1):2-12 (2000). Tumor necrosisfactor-alpha (TNF-α) is a major mediator of inflammation. Its importancein the pathogenesis of various forms of bone loss is supported byseveral lines of experimental and clinical evidence. Feldmann et al.,Cell, 85(3):307-310 (1996). However, TNF-α is not essential forosteoclastogenesis (Douni et al., J. Inflamm., 47:27-38 (1996)), erosivearthritis (Campbell et al., J. Clin. Invest., 107(12):1519-1527 (2001)),or osteolysis (Childs et al., J. Bon. Min. Res., 16:338-347 (2001)), asthese can occur in the absence of TNF-α.

In RA specifically, an immune response is thought to beinitiated/perpetuated by one or several antigens presenting in thesynovial compartment, producing an influx of acute inflammatory cellsand lymphocytes into the joint. Successive waves of inflammation lead tothe formation of an invasive and erosive tissue called pannus. Thiscontains proliferating fibroblast-like synoviocytes and macrophages thatproduce proinflammatory cytokines such as TNF-α and interleukin-1(IL-1). Local release of proteolytic enzymes, various inflammatorymediators, and osteoclast activation contributes to much of the tissuedamage. There is loss of articular cartilage and the formation of bonyerosions. Surrounding tendons and bursa may become affected by theinflammatory process. Ultimately, the integrity of the joint structureis compromised, producing disability.

The precise contributions of B cells to the immunopathogenesis of RA arenot completely characterized. However, there are several possiblemechanisms by which B cells may participate in the disease process.Silverman and Carson, Arthritis Res. Ther., 5 Suppl. 4: S1-6 (2003).

Historically, B cells were thought to contribute to the disease processin RA predominantly by serving as the precursors ofautoantibody-producing cells. A number of autoantibody specificitieshave been identified including antibodies to Type II collagen, andproteoglycans, as well as RFs. The generation of large quantities ofantibody leads to immune complex formation and the activation of thecomplement cascade. This in turn amplifies the immune response and mayculminate in local cell lysis. Increased RF synthesis and complementconsumption has been correlated with disease activity. The presence ofRF itself is associated with a more severe form of RA and the presenceof extra-articular features.

Evidence exists (Janeway and Katz, J. Immunol., 138:1051 (1998); Riveraet al., Int. Immunol., 13: 1583-1593 (2001)) showing that B cells arehighly efficient antigen-presenting cells (APC). RF-positive B cells maybe particularly potent APCs, since their surface immunoglobulin wouldreadily allow capture of any immune complexes regardless of the antigenspresent within them. Many antigens may thus be processed forpresentation to T cells. In addition, it has been recently suggestedthat this may also allow RF-positive B cells to self-perpetuate. Edwardset al., Immunology, 97: 188-196 (1999).

For activation of T cells, two signals need to be delivered to the cell;one via the T-cell receptor (TCR), which recognizes the processedpeptide in the presence of major histocompatibility complex (MHC)antigen, and a second, via co-stimulatory molecules. When activated, Bcells express co-stimulatory molecules on their surface and can thusprovide the second signal for T-cell activation and the generation ofeffector cells.

B cells may promote their own function as well as that of other cells byproducing cytokines. Harris et al., Nat. Immunol., 1: 475-482 (2000).TNF-α, IL-1, lymphotoxin-α, IL-6, and IL-10 are amongst some of thecytokines that B cells may produce in the RA synovium.

Although T-cell activation is considered to be a key component in thepathogenesis of RA, recent work using human synovium explants in severecombined immunodeficiency disorders (SCID) mice has demonstrated thatT-cell activation and retention within the joint is critically dependenton the presence of B cells. Takemura et al., J. Immunol., 167: 4710-4718(2001). The precise role of B cells in this is unclear, since other APCsdid not appear to have the same effect on T cells.

Structural damage to joints is an important consequence of chronicsynovial inflammation. Between 60% and 95% of patients with RA developat least one radiographic erosion within 3-8 years of disease onset.Paulus et al., J. Rheumatol., 23: 801-805 (1996); Hulsmans et al.,Arthritis Rheum., 43: 1927-1940 (2000). In early RA, the correlationbetween radiographic damage scores and functional capacity is weak, butafter 8 years of disease, correlation coefficients can reach as high as0.68. Scott et al., Rheumatology, 39:122-132 (2000). In 1,007 patientsyounger than age 60 years who had RA for at least four years, Wolfe etal. (Arthritis Rheum, 43 Suppl. 9:S403 (2000)) found a significantassociation among the rate of progression of the Larsen radiographicdamage score (Larsen et al., Acta Radiol. Diagn. 18:481-491 (1977)),increasing Social Security disability status, and decreasing familyincome.

Diagnosis of RA may be according to current American College ofRheumatology (ACR) criteria and may include morning stiffness in andaround the joints lasting for at least 1 hour before maximalimprovement; arthritis of three or more joint areas: at least threejoint areas have simultaneously had soft tissue swelling or fluid (notbony overgrowth alone) observed by a physician; the 14 possible jointareas (right and left) are proximal interphalangeal (PIP),metacarpophalangeal (MCP), wrist, elbow, knee, ankle, andmetatarsophalangeal (MTP) joints; arthritis of hand joints: at least onejoint area swollen as above in wrist, MCP, or PIP joint; symmetricarthritis: simultaneous involvement of the same joint areas (as inarthritis of three or more joint areas, above) on both sides of the body(bilateral involvement of PIP, MCP, or MTP joints is acceptable withoutabsolute symmetry); rheumatoid nodules: subcutaneous nodules over bonyprominences or extensor surfaces or in juxta-articular regions that areobserved by a physician; serum rheumatoid factor: demonstration ofabnormal amounts of serum rheumatoid factor by any method that has beenpositive in fewer than five percent of normal control patients;radiographic changes: radiographic changes typical of rheumatoidarthritis on posteroanterior hand and wrist X-rays, which must includeerosions or unequivocal bony decalcification localized to or most markedadjacent to the involved joints (osteoarthritis changes alone do notqualify). Diagnosis of RA is typically made if a patient satisfies atleast four of the above criteria.

In certain instances, a diagnosis of RA is made if a patient has aparticular Disease Activity Score (DAS) (see, e.g., Van der Heijde D. M.et al., J Rheumatol, 1993, 20(3): 579-81; Prevoo M. L. et al, ArthritisRheum, 1995, 38: 44-8). The DAS system represents both current state ofdisease activity and change. The DAS scoring system uses a weightedmathematical formula, derived from clinical trials in RA. For example,the DAS 28 is 0.56(T28)+0.28(SW28)+0.70(Ln ESR)+0.014 GH wherein Trepresents tender joint number, SW is swollen joint number, ESR iserythrocyte sedimentation rate, and GH is global health. Various valuesof the DAS represent high or low disease activity as well as remission,and the change and endpoint score result in a categorization of thepatient by degree of response (none, moderate, good).

A number of therapeutic agents, including biological agents, areavailable for the treatment of RA. Furst et al., Ann. Rheum. Dis.67:2-25 (2008). Prevention or retardation of radiographic damage is oneof the goals of RA treatment. Edmonds et al., Arthritis Rheum.,36:336-340 (1993). Controlled clinical trials of 6 or 12 months'duration have documented that the progression of radiographic damagescores was more rapid in the placebo group than in groups that receivedmethotrexate (MTX) (Sharp et al., Arthritis Rheum., 43: 495-505 (2000)),leflunomide (Sharp et al., supra), sulfasalazine (SSZ) (Sharp et al.,supra), prednisolone (Kirwan et al., N. Engl. J. Med., 333:142-146(1995); Wassenburg et al., Arthritis Rheum, 42: Suppl 9:S243 (1999)),interleukin-1 receptor antagonist (Bresnihan et al., Arthritis Rheum,41: 2196-2204 (1998)), or an infliximab/MTX combination. Lipsky et al.,N. Eng. J. Med., 343: 1594-1604 (2000). Clinical trials have alsodocumented that radiographic progression following treatment withetanercept was less rapid than that following treatment with MTX. Bathonet al., N. Engl. J. Med., 343:1586-1593 (2000). Other studies haveevaluated radiographic progression in patients treated withcorticosteroids (Joint Committee of the Medical Research Council andNuffield Foundation, Ann Rheum. Dis., 19:331-337 (1960); Van Everdingenet al., Ann. Intern. Med., 136:1-12 (2002)), cyclosporin A (Pasero etal., J. Rheumatol., 24:2113-2118 (1997); Forre, Arthritis Rheum.,37:1506-1512 (1994)), MTX versus azathioprine (Jeurissen et al., Ann.Intern. Med., 114:999-1004 (1991)), MTX versus auranofin (Weinblatt etal., Arthritis Rheum., 36:613-619 (1993)), MTX (meta-analysis) (Alarconet al., J. Rheumatol., 19:1868-1873 (1992)), hydroxychloroquine (HCQ)versus SSZ (Van der Heijde et al., Lancet, 1:1036-1038), SSZ (Hannonenet al., Arthritis Rheum., 36:1501-1509 (1993)), the COBRA(Combinatietherapei Bij Reumatoide Artritis) combination ofprednisolone, MTX, and SSZ (Boers et al., Lancet, 350:309-318 (1997);Landewe et al., Arthritis Rheum., 46: 347-356 (2002)), combinations ofMTX, SSZ, and HCQ (O'Dell et al., N. Engl. J. Med., 334:1287-1291(1996); Mottonen et al., Lancet, 353:1568-1573 (1999)), the combinationof cyclophosphamide, azathioprine, and HCQ (Csuka et al., JAMA,255:2115-2119 (1986)), and the combination of adalimumab with MTX.Keystone et al., Arthritis Rheum., 46 Suppl. 9:S205 (2002).

The FDA has now approved labeling claims that certain medications, e.g.,leflunomide, etanercept, and infliximab, slow the progression ofradiographic joint damage. These claims are based on the statisticallysignificant differences in progression rates observed between randomlyassigned treatment groups and control groups. However, the progressionrates in individuals within the treatment and control groups overlap toa considerable extent. Therefore, despite significant differencesbetween treatment groups, these data cannot be used to estimate theprobability that a patient who is starting a treatment will have afavorable outcome with respect to progression of radiographic damage.Various methods have been suggested to categorize paired radiographsfrom individual patients as not progressive, e.g., damage scores of 0 atboth time points, no increase in damage scores, no new joints witherosions, and a change in score not exceeding the smallest detectabledifference (i.e., 95% confidence interval for the difference betweenrepeated readings of the same radiograph). Lassere et al., J.Rheumatol., 26: 731-739 (1999).

Determining whether there has been increased structural damage in anindividual patient during the interval between paired radiographsobtained at the beginning and end of a or 12-month clinical trial hasbeen difficult, for several reasons. The rate of radiographic damage isnot uniform within a population of RA patients; a few patients may haverapidly progressing damage, but many may have little or no progression,especially if the tie interval is relatively short. The methods forscoring radiographic damage, e.g., Sharp (Sharp et al., ArthritisRheum., 14: 706-720 (1971); Sharp et al., Arthritis Rheum., 28:1326-1335 (1985)), Larsen (Larsen et al., Acta Radiol. Diagn., 18:481-491 (1977)), and modifications of these methods (Van der Heijde, J.Rheumatol., 27: 261-263 (2000)), depend on the judgment and theinterpretation of the reader as to what is real. Factors to determineare whether an apparent interruption of the subchondral cortical plateis real, or whether a decrease in the distance between the cortices onopposite sides of a joint is real, or is due to a slight change in theposition of the joint relative to the film and the radiographic beam, toa change in radiographic exposure, or to some other technical factor.

Therefore, the recorded score is an approximation of the true damage,and for many subjects, the smallest detectable difference between repeatscores of the same radiographs is larger than the actual change that hasoccurred during the interval between the baseline and final radiographs.If the reader is blinded to the temporal sequence of the films, theseunavoidable scoring errors may be in either direction, leading toapparent “healing” when the score decreases or to apparent rapidprogression when reading error increases the difference between films.When the study involves a sufficiently large population of patients whohave been randomly assigned to receive an effective treatment ascompared with placebo, the positive and negative reading errors offseteach other, and small but real differences between treatment groups canbe detected.

The imprecision of the clinical measures that are used to quantitate RAdisease activity has caused a similar problem. Statistically significantdifferences between certain outcome measures from clinical trials werenot useful for estimating the probability of improvement for anindividual who was starting the treatment. Paulus et al., ArthritisRheum., 33:477-484 (1990). Attribution of individual improvement becamepractical with the creation of the American College of Rheumatology(ACR) 20% composite criteria for improvement (ACR20), which designated apatient as improved if there was 20% improvement in the tender andswollen joint counts and 20% improvement in at least three of fiveadditional measures (pain, physical function, patient global healthassessment, physician global health assessment, and acute-phase reactantlevels). Felson et al., Arthritis Rheum., 38:727-735 (1995). All ofthese measures have large values for the smallest detectable difference,but by requiring simultaneous improvement in five of the seven aspectsof the same process (disease activity), the randomness of the sevenmeasurement errors is constrained, and it is easier to attribute realimprovement to the individual.

In RA, joint damage is a prominent feature. Radiologic parameters ofjoint destruction are seen as a key outcome measure in descriptions ofdisease outcome. In the recent OMERACT (Outcome Measures in RheumatologyClinical Trials) consensus meeting, radiology was chosen as part of thecore set of outcome measures for longitudinal observational studies.Wolfe et al., Arthritis Rheum., 41 Supp 9: S204 (1998) abstract.Radiology is also part of the WHO/ILAR (World HealthOrganization/International League of Associations for Rheumatology)required core set of measures for long-term clinical trials. Tugwell andBoers, J. Rheumatol., 20:528-530 (1993).

Available data on the outcome of radiologic damage in RA have beenobtained in both short-term and long-term studies. In short-term studiesof RA patients with recent-onset disease, radiographs obtained every sixmonths showed that after an initial rapid progression, there wasdiminution of the progression rate of radiologic damage in the hands andfeet after two to three years. Van der Heijde et al., Arthritis Rheum.,35: 26-34 (1992); Fex et al., Br. J. Rheumatol., 35: 1106-1055 (1996).In long-term studies with radiographs taken less frequently, a constantrate of progression was found, with relentless deterioration of damageup to 25 years of disease duration. Wolfe and Sharp, Arthritis Rheum.,41:1571-1582 (1998); Graudal et al., Arthritis Rheum., 41:1470-1480(1998); Plant et al., J. Rheumatol., 25:417-426 (1998); Kaarela andKautiainen, J. Rheumatol., 24:1285-1287 (1997). Whether thesedifferences in radiographic progression pattern are due to differencesin the scoring techniques is not clear.

The scoring systems used differ in the number of joints being scored,the presence of independent scores for erosions (ERO) and joint spacenarrowing (JSN), the maximum score per joint, and the weighing of aradiologic abnormality. As yet, there is no consensus on the scoringmethod of preference. During the first three years of follow-up in acohort study of patients with early arthritis, JSN and ERO were found todiffer in their contribution to the measured progression in radiologicdamage of the hands and feet. Van der Heijde et al., Arthritis Rheum.,35:26-34 (1992). Furthermore, methods that independently score ERO andJSN, such as the Sharp and Kellgren scores, were found to be moresensitive to change in early RA than methods using an overall measure,such as the Larsen score. Plant et al., J. Rheumatol., 21:1808-1813(1994); Cuchacovich et al., Arthritis Rheum., 35:736-739 (1992). TheSharp score is a very labor-intensive method. Van der Heijde, BaillieresClin. Rheumatol., 10:435-533 (1996). In late or destructive RA, theSharp and the Larsen methods were found to provide similar information.However, the sensitivity to change of the various scoring methods latein the disease has not yet been investigated, and it can be argued thatthe scoring methods that independently measure ERO and JSN provideuseful information. Pincus et al., J. Rheumatol., 24:2106-2122 (1997).See also Drossaers-Bakker et al., Arthritis Rheum., 43:1465-1472 (2000),which compared the three radiologic scoring systems for the long-termassessment of RA. Paulus et al., Arthritis Rheum., 50: 1083-1096 (2004)categorized radiographic joint damage as progressive or non-progressivein individuals with RA participating in clinical trials, and concludedthat RA joint damage in an observational cohort can be classified asprogressive or non-progressive with the use of a composite definitionthat includes a number of imprecise and related, but distinct, measuresof structural joint damage. It appears that in day-to-day clinicalmanagement of an RA patient, an interval change between a pair ofradiographs of at least five Sharp radiographic damage score unitsshould be present before one considers the structural change to be realand uses it as the basis for a treatment decision.

Certain RA Therapeutic Agents

Initial therapy of RA typically involves administration of one or moreof the following drugs: nonsteroidal antiinflammatory drugs (NSAIDs),e.g., acetylsalicylic acid (e.g., aspirin), ibuprofen (Motrin), naproxen(Naprosyn), indomethacin (Indocin), nabumetone (Relafen), tolmetin(Tolectin); glucocorticoid (via joint injection); and low-doseprednisone. See “Guidelines for the management of rheumatoid arthritis,”Arthritis & Rheumatism 46(2): 328-346 (February, 2002). The majority ofpatients with newly diagnosed RA are started with disease-modifyingantirheumatic drug (DMARD) therapy within 3 months of diagnosis. DMARDscommonly used in RA are hydroxychloroquine, sulfasalazine, methotrexate(plus oral and subcutaneous methotrexate), leflunomide, azathioprine,D-penicillamine, Gold (oral), Gold (intramuscular), minocycline,cyclosporine, Staphylococcal protein A immunoadsorption. In certaininstances, patients are treated with immunomodulating agents such asazathioprine or cyclophosphamide. Additional RA therapeutic agentsinclude an anti-cytokine agent (e.g., anti-tumor necrosis factor α,anti-interleukin-1-receptor (e.g., anakinra), anti-interleukin 10,anti-interleukin 6 receptor, anti-interleukin 6, anti-interferon alpha,anti-B-lymphocyte stimulator), an inhibitor of costimulation (e.g.,anti-CD154, CTLA4-Ig (e.g., abatacept)).

In certain instances, TNFα inhibitors have been used for therapy of RA.Exemplary TNFα inhibitors include etanercept (sold under the trade nameENBREL®), infliximab (sold under the trade name REMICADE®), adalimumab(sold under the trade name HUMIRA®), golimumab (sold under the tradename SIMPONI™) and certolizumab pegol (sold under the trade nameCIMZIA®).

Etanercept (sold under the trade name ENBREL®) is an injectable drugapproved in the U.S. for therapy of active RA. Etanercept binds to TNFαand serves to remove most TNFα from joints and blood, thereby preventingTNFα from promoting inflammation and other symptoms of rheumatoidarthritis. Etanercept is an “immunoadhesin” fusion protein consisting ofthe extracellular ligand binding portion of the human 75 kD (p75) tumornecrosis factor receptor (TNFR) linked to the Fc portion of a humanIgG1. The drug has been associated with negative side effects includingserious infections and sepsis, and nervous system disorders such asmultiple sclerosis (MS). See, e.g.,www.remicade-infliximab.com/pages/enbrel_embrel.html.

Infliximab, sold under the trade name REMICADE®, is animmune-suppressing drug prescribed to treat RA and Crohn's disease.Infliximab is a chimeric monoclonal antibody that binds to TNFα andreduces inflammation in the body by targeting and binding to TNFα whichproduces inflammation. Infliximab has been linked to certain fatalreactions such as heart failure and infections including tuberculosis aswell as demyelination resulting in MS. See, e.g.,www.remicade-infliximab.com.

In 2002, Abbott Laboratories received FDA approval to market adalimumab(sold under the trade name HUMIRA®), previously known as D2E7.Adalimumab is a human monoclonal antibody that binds to TNFα and isapproved for reducing the signs and symptoms and inhibiting theprogression of structural damage in adults with moderately to severelyactive RA who have had insufficient response to one or more traditionaldisease modifying DMARDs.

In April 2009, Centocor Ortho Biotech Inc. received FDA approval tomarket golimumab (sold under the trade name SIMPONI™) for patients withmoderate to severe RA, psoriatic arthritis, and ankylosing spondylitis.Golimumab is a human IgG1κ monoclonal antibody specific for human TNFαand which is self-administered by patients subcutaneously once everymonth. Golimumab binds to both soluble and transmembrane bioactive formsof TNFα. Similar to other agents that inhibit TNFα, golimumab has beenassociated with certain adverse events such as risk of infection,including serious and life-threatening fungal infections.

In May 2009, certolizumab pegol (sold under the trade name CIMZIA®) wasapproved by the FDA for treatment of patients with RA. It isadministered by a healthcare professional by subcutaneous injectionevery two weeks during induction and then every four weeks duringmaintenance. Certolizumab pegol is a recombinant, humanized antibodyFab′ fragment, with specificity for human TNFα, conjugated to anapproximately 40 kDa polyethylene glycol (PEG2MAL40K). Certolizumabpegol has also been associated with certain safety risks such asincreased risk of serious infection, similar to other TNFα inhibitors.

In certain instances, the rituximab antibody (sold under the trade nameRITUXAN®) has been used as a therapy for RA. Rituximab is a geneticallyengineered chimeric murine/human monoclonal antibody directed againstthe CD20 antigen. Rituximab is the antibody called “C2B8” in U.S. Pat.No. 5,736,137 issued Apr. 7, 1998 (Anderson et al.).

Another anti-CD20 antibody is ocrelizumab. Ocrelizumab is a humanizedvariant of an anti-CD20 antibody, 2H7. Such humanized 2H7 variants aredescribed, for example, in International Publication No. WO 2004/056312(International Application No. PCT/US2003/040426).

RA therapeutic agents having B-cell antagonist activity can beidentified, for example, by screening compounds for certain biologicalproperties. For example, a method of screening can be employed asdescribed in Sundberg et al., Cancer Research 66, 1775-1782 (2006)wherein a compound was screened for inhibition of B-cell proliferationby targeting c-myc protein for rapid and specific degradation. See alsoMackay et al., Annual Review of Immunology, 21: 231-264 (2003) regardingBAFF, APRIL, and a tutorial on B-cell survival and screening, andThangarajh et al., Scandinavian J. Immunol., 65(1):92 (2007) on B-cellproliferation and APRIL. In addition, Sakurai et al., European J.Immunol., 37(1):110 (2007) discloses that TACI attenuates antibodyproduction co-stimulated by BAFF-R and CD40. Further, Acosta-Rodriguezet al., European J. Immunol., 37(4):990 (2007) discloses that BAFF andLPS cooperate to induce B cells to become susceptible toCD95/Fas-mediated cell death. Further screening methods can be found inMartin and Chan, “B Cell Immunobiology in Disease: Evolving Conceptsfrom the Clinic Annual Review of Immunology,” 24:467-496 (2006), Pillaiet al., “Marginal Zone B Cells” Annual Review of Immunology, 23:161-196(2005), and Hardy and Hayakawa, “B Cell Development Pathways,” AnnualReview of Immunology, 19:595-621 (2001). From these and other referencesthe skilled artisan can screen for the appropriate antagonists.Microarrays can be used for this purpose (Hagmann, Science, 290:82-83(2000)), as well as RNA interference (RNAi) (Ngo et al., Nature,441:106-110 (2006)).

B-cell antagonists included within the scope of the present inventioninclude antibodies, synthetic or native-sequence peptides,immunoadhesins, and small-molecule antagonists that bind to a B-cellsurface marker or a B-cell specific survival or proliferation factor,optionally conjugated with or fused to another molecule. In certainembodiments, the antagonist comprises an antibody or immunoadhesin. Itincludes BLyS antagonists such as immunoadhesins, including, but notlimited to, anti-CD23 (e.g., lumiliximab), anti-CD20, anti-CD22, oranti-BR3 antibodies, APRIL antagonists, and/or BLyS immunoadhesins. Incertain embodiments, the BLyS immunoadhesin is selected from BR3immunoadhesin comprising the extracellular domain of BR3, TACTimmunoadhesin comprising the extracellular domain of TACI, and BCMAimmunoadhesin comprising the extracellular domain of BCMA. Certainembodiments of BR3 immunoadhesin include hBR3-Fc as described in WO2005/00351, U.S. Pat. Pub. No. 2005/0095243, U.S. Pat. Pub. No.2005/0163775 and WO 2006/068867. In certain embodiments, the BLySantagonist is an anti-BLyS antibody, wherein the anti-BLyS antibodybinds BLyS within a region of BLyS comprising residues 162-275, or ananti-BR3 antibody, wherein the anti-BR3 antibody binds BR3 in a regioncomprising residues 23-38 of human BR3. In certain embodiments, theimmunoadhesins are selected from TACI-Ig (atacicept) and BR3-Ig. Incertain embodiments, the B-cell antagonist is to CD20, CD22, BAFF, orAPRIL. In certain such embodiments, the antagonist is an antibody orTACI-Ig.

The CD22 antigen, or CD22, also known as BL-CAM or Lyb8, is a type 1integral membrane glycoprotein with molecular weight of about 130(reduced) to 140 kD (unreduced). It is expressed in both the cytoplasmand cell membrane of B-lymphocytes. CD22 antigen appears early in B-celllymphocyte differentiation at approximately the same stage as the CD19antigen. Unlike certain other B-cell markers, CD22 membrane expressionis limited to the late differentiation stages comprised between mature Bcells (CD22+) and plasma cells (CD22−). The CD22 antigen is described,for example, in Wilson et al., J. Exp. Med., 173:137 (1991) and Wilsonet al., J. Immunol., 150:5013 (1993).

Certain exemplary anti-CD22 antibodies include those described in EP1,476,120 (Tedder and Tuscano), EP 1,485,130 (Tedder), and EP 1,504,035(Popplewell et al.), as well as those described in U.S. Pat. Pub. No.2004/0258682 (Leung et al.), U.S. Pat. No. 5,484,892 (Dana-Farber), U.S.Pat. No. 6,183,744 (Immunomedics, epratuzumab), and U.S. Pat. No.7,074,403 (Goldenberg and Hansen).

BLyS (also known as BAFF, TALL-1, THANK, TNFSF13B, or zTNF4) is a memberof the TNF1 ligand superfamily that is essential for B-cell survival andmaturation. BAFF overexpression in transgenic mice leads to B-cellhyperplasia and development of severe autoimmune disease (Mackay et al.,J. Exp. Med., 190:1697-1710 (1999); Gross et al., Nature, 404:995-999(2000); Khare et al., Proc. Natl. Acad. Sci. U.S.A, 97:3370-3375(2000)). BAFF levels are elevated in human patients with a variety ofautoimmune disorders, such as SLE, RA, and Sjögren's syndrome (Cheema etal., Arthritis Rheum., 44:1313-1319 (2001); Groom et al, J. Clin.Invest., 109:59-68 (2002); Zhang et al., J. Immunol., 166:6-10 (2001)).Furthermore, BAFF levels correlate with disease severity, suggestingthat BAFF can play a direct role in the pathogenesis of these illnesses.BAFF acts on B cells by binding to three members of the TNF receptorsuperfamily, TACI, BCMA, and BR3 (also known as BAFF-R) (Gross et al.,supra; Thompson et al., Science, 293:2108-2111 (2001); Yan et al., Curr.Biol. 11:1547-1552 (2001); Yan et al., Nat. Immunol., 1:37-41 (2000);Schiemann et al., Science, 293:2111-2114 (2001)).

Of the three, only BR3 is specific for BAFF; the other two also bind therelated TNF family member, A proliferation-inducing ligand (APRIL).Comparison of the phenotypes of BAFF and receptor knockout or mutantmice indicates that signaling through BR3 mediates the B-cell survivalfunctions of BAFF (Thompson et al., supra; Yan et al., supra, 2001;Schiemann et al., supra). In contrast, TACI appears to act as aninhibitory receptor (Yan, Nat. Immunol., 2:638-643 (2001)), while therole of BCMA is unclear (Schiemann et al., supra). US 2007/0071760discloses treating B-cell malignancies using a TACI-Ig fusion moleculein an amount sufficient to suppress proliferation-inducing functions ofBlyS and APRIL.

BR3 is a 184-residue type III transmembrane protein expressed on thesurface of B cells (Thompson et al., supra; Yan, Nat. Immun., supra).The intracellular region bears no sequence similarity to knownstructural domains or protein-protein interaction motifs. Nevertheless,BAFF-induced signaling through BR3 results in processing of thetranscription factor NF-B2/p100 to p52 (Claudio et al., Nat. Immunol.,3:958-965 (2002); Kayagaki et al., Immunity, 10:515-524 (2002)). Theextracellular domain (ECD) of BR3 is also divergent. TNFR family membersare usually characterized by the presence of multiple cysteine-richdomains (CRDs) in their extracellular region; each CRD is typicallycomposed of about 40 residues stabilized by six cysteines in threedisulfide bonds. Conventional members of this family make contacts withligand through two CRDs interacting with two distinct patches on theligand surface (Bodmer et al., Trends Biochem. Sci., 27:19-26 (2002)).However, the BR3ECD contains only four cysteine residues, capable offorming a partial CRD at most, raising the question of how such a smallreceptor imparts high-affinity ligand binding.

It has been shown that the BAFF-binding domain of BR3 resides within a26-residue core region (Kayagaki et al., supra). Six BR3 residues, whenstructured within a β-hairpin peptide (bhpBR3), were sufficient toconfer BAFF binding and block BR3-mediated signaling. Others havereported polypeptides purported to interact with BAFF (e.g., WO2002/24909, WO 2003/035846, WO 2002/16312, and WO 2002/02641).

Loss of function and radiographic change occur early in the course ofthe disease. These changes can be delayed or prevented with the use ofcertain DMARDs. Although several DMARDs are initially clinicallyeffective and well tolerated, many of these drugs become less effectiveor exhibit increased toxicity over time. Based on its efficacy andtolerability, MTX has become the standard therapy by which othertreatments are measured. Bathon et al., N. Eng. J. Med., 343:1586-1593(2000); Albert et al., J. Rheumatol., 27:644-652 (2000).

Recent studies have examined radiographic progression in patients withlate-stage RA who have taken leflunomide, MTX, or placebo (Strand etal., Arch. Intern. Med., 159:2542-2550 (1999)) as well as patients whohave taken infliximab plus MTX or placebo plus MTX following a partialresponse to MTX. Lipsky et al., N. Engl. J. Med., 343:1594-1602 (2000);Maini et al., Lancet, 354:1932-1939 (1999). In the first year of theENBREL™ ERA (early RA) trial, etanercept was shown to be significantlymore effective than MTX in improving signs and symptoms of disease andin inhibiting radiographic progression. Bathon et al., N. Eng. J. Med.,343:1586-1593 (2000). Genovese et al., Arthritis Rheum. 46: 1443-1450(2002) reports results from the second year of the study, concludingthat etanercept as monotherapy was safe and superior to MTX in reducingdisease activity, arresting structural damage, and decreasing disabilityover two years in patients with early aggressive RA. Also studied wasthe safety and clinical activity of ocrelizumab (a humanized antibodytargeting C D20+B cells) in combination with MTX in moderate-to-severeRA patients (Ph I/II ACTION study). Genovese et al., Arthritis Rheum.,54(9):S66-S67 (September 2006).

Further, reduction in radiographic progression in the hands and feet wasobserved in patients with early RA after receiving infliximab incombination with MTX. Van der Heijde et al., Annals Rheumatic Diseases,64:417 (2005). Patients with early RA achieved a clinically meaningfuland sustained improvement in physical function after treatment withinfliximab. Smolen et al., Annals Rheumatic Diseases, 64:418-419 (2005).

The effect of infliximab therapy on bone mineral density in patientswith ankylosing spondylitis (AS) resulting from a randomized,placebo-controlled trial named ASSERT) is reported by Van der Heijde etal., Annals Rheumatic Diseases, 64:319 (2005). The ASSERT trial showedthat infliximab improved fatigue and pain in patients with AS. Van derHeijde et al., Annals Rheumatic Diseases, 64:318-319 (2005). Theefficacy and safety of infliximab in AS patients treated according toASSERT are described by van der Heijde et al., Arthritis Rheum.,5:582-591 (2005). The authors conclude that infliximab was welltolerated and effective in a large cohort of patients with AS during a24-week study period. In addition, the effect of infliximab therapy onspinal inflammation was assessed by magnetic resonance imaging in arandomized, placebo-controlled trial of 279 patients with AS. Van derHeijde et al., Annals Rheumatic Diseases, 64:317 (2005). The manner inwhich the treatment effect on spinal radiographic progression inpatients with AS should be measured is addressed by van der Heijde etal., Arthritis Rheum. 52:1979-1985 (2005).

The results of radiographic analyses of the infliximab multinational PsAcontrolled trial (IMPACT) after one year are reported by Antoni et al.,Annals Rheumatic Diseases 64:107 (2005). Evidence of radiographicbenefit of treatment with infliximab plus MTX in RA patients who had noclinical improvement, with a detailed subanalysis of data from theanti-TNF trial in RA with concomitant therapy study, is reported bySmolen et al., Arthritis Rheum. 52:1020-1030 (2005). Radiographicprogression (as measured by mean change in modified Sharp/van der Heijdescore) was much greater in patients receiving MTX plus placebo than inpatients receiving infliximab plus MTX. The authors conclude that evenin patients without clinical improvement, treatment with infliximab plusMTX provided significant benefit with regard to the destructive process,suggesting that in such patients these two measures of disease aredissociated. The association between baseline radiographic damage andimprovement in physical function after treatment of patients having RAwith infliximab is described by Breedveld et al., Annals RheumaticDiseases, 64:52-55 (2005). Structural damage was assessed using the vander Heijde modification of the Sharp score. The authors conclude thatgreater joint damage at baseline was associated with poorer physicalfunction at baseline and less improvement in physical function aftertreatment, underlining the importance of early intervention to slow theprogression of joint destruction.

Rheumatoid Arthritis Molecular Biomarkers

A number of investigators have carried out microarray gene expressionprofiling studies of synovial tissue isolated from RA patients. Thepublished studies include van der Pouw Kraan T C et al., Discovery ofdistinctive gene expression profiles in rheumatoid synovium using cDNAmicroarray technology: evidence for the existence of multiple pathwaysof tissue destruction and repair, Genes Immun April; 4(3):187-96 (2003);van der Pouw Kraan T C, et al., Rheumatoid arthritis is a heterogeneousdisease: evidence for differences in the activation of the STAT-1pathway between rheumatoid tissues, Arthritis Rheum August;48(8):2132-45 (2003); Finis K et al., Analysis of pigmented villonodularsynovitis with genome-wide complementary DNA microarray and tissue arraytechnology reveals insight into potential novel therapeutic approaches,Arthritis Rheum March; 54(3):1009-19 (2006); Lindberg J, et al., Effectof infliximab on mRNA expression profiles in synovial tissue ofrheumatoid arthritis patients, Arthritis Res Ther. 8(6):R179 (2006); vander Pouw Kraan T C et al., Responsiveness to anti-tumour necrosis factoralpha therapy is related to pre-treatment tissue inflammation levels inrheumatoid arthritis patients, Ann Rheum Dis. April; 67(4):563-6 (2008);Huber R et al., Identification of intra-group, inter-individual, andgene-specific variances in mRNA expression profiles in the rheumatoidarthritis synovial membrane, Arthritis Res Ther 10(4):R98 (2008); BadotV et al., Gene expression profiling in the synovium identifies apredictive signature of absence of response to adalimumab therapy inrheumatoid arthritis, Arthritis Res Ther. 11(2):R57 (2009), Epub 2009Apr. 23.

International Patent Application No. PCT/US2010/047734 (Intn'l Pub. No.WO2011/028945) describes a statistically rigorous interrogation ofgenome-wide transcription in a large set of RA synovial tissues. RAjoints were stratified into four molecular phenotypes that differedtranscriptionally but not in disease duration, radiographic state orsystemic measures of inflammation. Meta-analysis revealed that eachphenotype expressed distinct transcriptional programs reflectingbiological differences with pathological relevance. Gene expressionmodules were developed for each phenotype, refined using statisticallearning procedures and validated on independent data sets. In addition,phenotype-intrinsic modules were used to identify molecular biomarkersto stratify new patients into subtypes of RA with predictable responsesto B cell targeted therapy, such as anti-CD20 monoclonal antibodies.

Multiple Sclerosis and Certain Therapeutic Agents

Multiple Sclerosis (MS) is a disorder of the central nervous system thataffects the brain and spinal cord. MS generally exhibits arelapsing-remitting course or a chronic progressive course.Relapsing-remitting MS (RRMS) is characterized by partial or totalrecovery after attacks. Secondary-progressive MS (SPMS) is arelapsing-remitting course which becomes steadily progressive. Attacksand partial recoveries may continue to occur. Primary-progressive MS(PPMS) is progressive from the onset. Symptoms in patients with PPMSgenerally do not remit—i.e., decrease in intensity.

Common signs and symptoms of MS include paresthesias in one or moreextremities, in the trunk, or on one side of the face; weakness orclumsiness of a leg or hand; or visual disturbances (such as partialblindness and pain in one eye), dimness of vision, or scotomas. Othercommon early symptoms are ocular palsy resulting in double vision(diplopia), transient weakness of one or more extremities, slightstiffness or unusual fatigability of a limb, minor gait disturbances,difficulty with bladder control, vertigo, and mild emotionaldisturbances (Berkow et al. (ed.), 1999, Merck Manual of Diagnosis andTherapy: 17th Ed). The etiology of MS is unknown, however, viralinfections, genetic predisposition, environment, and autoimmunity allappear to contribute to the disorder. Lesions in MS patients containinfiltrates of predominantly T lymphocyte mediated microglial cells andinfiltrating macrophages. CD4+ T lymphocytes are the predominant celltype present at these lesions. The hallmark of the MS lesion is plaque,an area of demyelination sharply demarcated from the usual white matterseen in MRI scans. Histological appearance of MS plaques varies withdifferent stages of the disease. In active lesions, the blood-brainbarrier is damaged, thereby permitting extravasation of serum proteinsinto extracellular spaces. Inflammatory cells can be seen inperivascular cuffs and throughout white matter. CD4− T-cells, especiallyTh1, accumulate around postcapillary venules at the edge of the plaqueand are also scattered in the white matter. In active lesions,up-regulation of adhesion molecules and markers of lymphocyte andmonocyte activation, such as IL2-R and CD26 have also been observed.Demyelination in active lesions is not accompanied by destruction ofoligodendrocytes. In contrast, during chronic phases of the disease,lesions are characterized by a loss of oligodendrocytes and hence, thepresence of myelin oligodendrocyte glycoprotein (MOG) antibodies in theblood. Current treatments for MS include corticosteroids, betainterferons (BETAFERON®, AVONEX®, REBIF®), glatiramer acetate(COPAXONE®), methotrexate, azathioprine, cyclophosphamide, cladribine,baclofen, tizanidine, amitriptyline, carbamazepine (Berkow et al. (ed.),1999, supra) and natalizumab (TYSABRI®).

ANCA-Vasculitis and Certain Therapeutic Agents

Wegener's granulomatosis and microscopic polyangiitis are classified asantineutrophil cytoplasmic antibody (ANCA)—associated vasculitidesbecause most patients with generalized disease have antibodies againstproteinase 3 or myeloperoxidase. (Jennette J C et al., Arthritis Rheum37:187-192 (1994); Finkielman J D et al., Am J Med 120(7):643.e9-643.14(2007)) The ANCA-associated vasculitides affect small-to-medium-sizeblood vessels, with a predilection for the respiratory tract andkidneys. (Hoffman G S et al., Ann Intern Med 116:488-498 (1992);Guillevin L et al., Arthritis Rheum 42:421-430 (1999); Reinhold-Keller Eet al., Arthritis Rheum 43:1021-1032 (2000); Stone J H. Arthritis Rheum48:2299-2309 (2003)). Cyclophosphamide and glucocorticoids have been thestandard therapy for remission induction for nearly four decades.(Novack S N et al., N Engl J Med 284:938-942 (1971); Fauci A S et al.,Medicine (Baltimore) 52:535-561 (1973)). This regimen transformed theusual treatment outcome of severe ANCA-associated vasculitis from deathto a strong likelihood of disease control and temporary remission.(Hoffman G S et al., supra; Guillevin L et al., supra; Reinhold-Kellersupra; Walton E W., BMJ 2:265-270 (1958); Jayne D et al., N Engl J Med349:36-44 (2003); The Wegener's Granulomatosis Etanercept Trial (WGET)Research Group, N Engl J Med 352:351-361 (2005). However, not allpatients have a remission with this combination of drugs, and those whodo often have disease flares that require repeated treatment. Moreover,side effects of cyclophosphamide, including infertility, cytopenias,infections, bladder injury, and cancer, as well as the multiple adverseeffects of lengthy courses of glucocorticoid treatment, are major causesof long-term disease and death. (Hoffman G S et al., supra; Guillevin Let al., supra; Reinhold-Keller supra; Jayne et al., supra; WGET supra;Stone J H, et al., Arthritis Rheum 54:1608-1618 (2006); Pagnoux C, etal., Arthritis Rheum 58:2908-2918 (2008)).

A number of studies have shown that rituximab demonstrates clinicalactivity in Wegener's granulomatosis and ANCA-vasculitis. For example,Specks et al. disclosed successful use of four infusions of 375 mg/m² ofrituximab and high-dose glucocorticoids to treat Wegener'sgranulomatosis. (Specks et al. Arthritis & Rheumatism, 44(12):2836-2840(2001)). In another study rituximab was found to be a well-tolerated,effective remission induction agent for severe ANCA-associatedvasculitis, when used in a dose of 375 mg/m²×four along with oralprednisone at 1 mg/kg/day, which was reduced to 40 mg/day by week four,and to total discontinuation over the following 16 weeks. Four patientswere re-treated with rituximab alone for recurring/rising ANCA titers.Other than glucocorticoids, no additional immunosuppressive agents seemnecessary for remission induction and maintenance of sustained remission(six months or longer). Keogh et al., Kidney Blood Press. Res., 26:293(2003) reported that eleven patients with refractory ANCA-associatedvasculitis went into remission upon treatment with four weekly 375 mg/m²doses of rituximab and high-dose glucocorticoids. Patients withrefractory ANCA-associated vasculitis were administered rituximab alongwith immunosuppressive medicaments such as intravenous CTX,mycophenolate mofetil, azathioprine, or leflunomide, with apparentefficacy. See also, Eriksson, “Kidney and Blood Pressure Research,26:294 (2003) (five patients with ANCA-associated vasculitis treatedwith rituximab 375 mg/m² once a week for four weeks responded to thetreatment); Jayne et al., Kidney and Blood Pressure Research, 26:294-295(2003) (six patients with refractory vasculitis receiving four weeklyinfusions of rituximab at 375 mg/m² with CTX along with backgroundimmunosuppression and prednisolone experienced major falls in vasculiticactivity). A further report of using rituximab along with intravenousCTX at 375 mg/m² per dose in four doses for administering to patientswith refractory systemic vasculitis is provided in Smith and Jayne, “Aprospective, open label trial of B-cell depletion with rituximab inrefractory systemic vasculitis” poster 998 (11^(th) InternationalVasculitis and ANCA workshop), American Society of Nephrology, J. Am.Soc. Nephrol., 14:755 A (2003). See also Eriksson, J. Internal Med.,257:540-548 (2005) regarding nine patients with ANCA-positive vasculitiswho were successfully treated with two or four weekly doses of 500 mg ofrituximab; and Keogh et al., Arthritis and Rheumatism, 52:262-268(2005), who reported that in 11 patients with refractory ANCA-associatedvasculitis, treatment or re-treatment with four weekly 375 mg/m² dosesof rituximab induced remission by B-lymphocyte depletion (studyconducted from January 2000 to September 2002). More recently, Stone etal. reported noninferiority of rituximab therapy (375 mg/m² per week for4 weeks) compared to cyclosphosphamide treatment for induction ofremission in severe ANCA-associated vasculitis and possible superiorityin relapsing disease. (Stone et al., N. England J. Med. 363(3):221-231(2010)).

Certain Additional Autoimmune Diseases

An autoimmune disease can be an organ-specific disease (i.e., the immuneresponse is specifically directed against an organ system such as theendocrine system, the hematopoietic system, the skin, thecardiopulmonary system, the gastrointestinal and liver systems, therenal system, the thyroid, the ears, the neuromuscular system, thecentral nervous system, etc.) or a systemic disease which can affectmultiple organ systems (for example, systemic lupus erythematosus (SLE),rheumatoid arthritis, polymyositis, etc.). Exemplary diseases includeautoimmune rheumatologic disorders (such as, for example, rheumatoidarthritis, Sjögren's syndrome, scleroderma, lupus such as SLE and lupusnephritis, polymyositis/dermatomyositis, cryoglobulinemia,anti-phospholipid antibody syndrome, and psoriatic arthritis),autoimmune gastrointestinal and liver disorders (such as, for example,inflammatory bowel diseases (e.g., ulcerative colitis and Crohn'sdisease), autoimmune gastritis and pernicious anemia, autoimmunehepatitis, primary biliary cirrhosis, primary sclerosing cholangitis,and celiac disease), vasculitis (such as, for example, ANCA-negativevasculitis and ANCA-associated vasculitis, including Churg-Straussvasculitis, Wegener's granulomatosis, and microscopic polyangiitis),autoimmune neurological disorders (such as, for example, multiplesclerosis, opsoclonus myoclonus syndrome, myasthenia gravis,neuromyelitis optica, Parkinson's disease, Alzheimer's disease, andautoimmune polyneuropathies), renal disorders (such as, for example,glomerulonephritis, Goodpasture's syndrome, and Berger's disease),autoimmune dermatologic disorders (such as, for example, psoriasis,urticaria, hives, pemphigus vulgaris, bullous pemphigoid, and cutaneouslupus erythematosus), hematologic disorders (such as, for example,thrombocytopenic purpura, thrombotic thrombocytopenic purpura,post-transfusion purpura, and autoimmune hemolytic anemia),atherosclerosis, uveitis, autoimmune hearing diseases (such as, forexample, inner ear disease and hearing loss), Behcet's disease,Raynaud's syndrome, organ transplant, and autoimmune endocrine disorders(such as, for example, diabetic-related autoimmune diseases such asinsulin-dependent diabetes mellitus (IDDM), Addison's disease, andautoimmune thyroid disease (e.g., Graves' disease and thyroiditis)).

Specific examples of other autoimmune disorders as defined herein, whichin some cases encompass those listed above, include, but are not limitedto, arthritis (acute and chronic, rheumatoid arthritis includingjuvenile-onset rheumatoid arthritis and stages such as rheumatoidsynovitis, gout or gouty arthritis, acute immunological arthritis,chronic inflammatory arthritis, degenerative arthritis, type IIcollagen-induced arthritis, infectious arthritis, Lyme arthritis,proliferative arthritis, psoriatic arthritis, Still's disease, vertebralarthritis, osteoarthritis, arthritis chronica progrediente, arthritisdeformans, polyarthritis chronica primaria, reactive arthritis,menopausal arthritis, estrogen-depletion arthritis, and ankylosingspondylitis/rheumatoid spondylitis), autoimmune lymphoproliferativedisease, inflammatory hyperproliferative skin diseases, psoriasis suchas plaque psoriasis, gutatte psoriasis, pustular psoriasis, andpsoriasis of the nails, atopy including atopic diseases such as hayfever and Job's syndrome, dermatitis including contact dermatitis,chronic contact dermatitis, exfoliative dermatitis, allergic dermatitis,allergic contact dermatitis, hives, dermatitis herpetiformis, nummulardermatitis, seborrheic dermatitis, non-specific dermatitis, primaryirritant contact dermatitis, and atopic dermatitis, x-linked hyper IgMsyndrome, allergic intraocular inflammatory diseases, urticaria such aschronic allergic urticaria and chronic idiopathic urticaria, includingchronic autoimmune urticaria, myositis, polymyositis/dermatomyositis,juvenile dermatomyositis, toxic epidermal necrolysis, scleroderma(including systemic scleroderma), sclerosis such as systemic sclerosis,multiple sclerosis (MS) such as spino-optical MS, primary progressive MS(PPMS), and relapsing remitting MS (RRMS), progressive systemicsclerosis, atherosclerosis, arteriosclerosis, sclerosis disseminata,ataxic sclerosis, neuromyelitis optica (NMO), inflammatory bowel disease(IBD) (for example, Crohn's disease, autoimmune-mediatedgastrointestinal diseases, gastrointestinal inflammation, colitis suchas ulcerative colitis, colitis ulcerosa, microscopic colitis,collagenous colitis, colitis polyposa, necrotizing enterocolitis, andtransmural colitis, and autoimmune inflammatory bowel disease), bowelinflammation, pyoderma gangrenosum, erythema nodosum, primary sclerosingcholangitis, respiratory distress syndrome, including adult or acuterespiratory distress syndrome (ARDS), meningitis, inflammation of all orpart of the uvea, iritis, choroiditis, an autoimmune hematologicaldisorder, graft-versus-host disease, angioedema such as hereditaryangioedema, cranial nerve damage as in meningitis, herpes gestationis,pemphigoid gestationis, pruritis scroti, autoimmune premature ovarianfailure, sudden hearing loss due to an autoimmune condition,IgE-mediated diseases such as anaphylaxis and allergic and atopicrhinitis, encephalitis such as Rasmussen's encephalitis and limbicand/or brainstem encephalitis, uveitis, such as anterior uveitis, acuteanterior uveitis, granulomatous uveitis, nongranulomatous uveitis,phacoantigenic uveitis, posterior uveitis, or autoimmune uveitis,glomerulonephritis (GN) with and without nephrotic syndrome such aschronic or acute glomerulonephritis such as primary GN, immune-mediatedGN, membranous GN (membranous nephropathy), idiopathic membranous GN oridiopathic membranous nephropathy, membrano- or membranous proliferativeGN (MPGN), including Type I and Type II, and rapidly progressiveGN(RPGN), proliferative nephritis, autoimmune polyglandular endocrinefailure, balanitis including balanitis circumscripta plasmacellularis,balanoposthitis, erythema annulare centrifugum, erythema dyschromicumperstans, eythema multiform, granuloma annulare, lichen nitidus, lichensclerosus et atrophicus, lichen simplex chronicus, lichen spinulosus,lichen planus, lamellar ichthyosis, epidermolytic hyperkeratosis,premalignant keratosis, pyoderma gangrenosum, allergic conditions andresponses, food allergies, drug allergies, insect allergies, rareallergic disorders such as mastocytosis, allergic reaction, eczemaincluding allergic or atopic eczema, asteatotic eczema, dyshidroticeczema, and vesicular palmoplantar eczema, asthma such as asthmabronchiale, bronchial asthma, and auto-immune asthma, conditionsinvolving infiltration of T cells and chronic inflammatory responses,immune reactions against foreign antigens such as fetal A-B-O bloodgroups during pregnancy, chronic pulmonary inflammatory disease,autoimmune myocarditis, leukocyte adhesion deficiency, lupus, includinglupus nephritis, lupus cerebritis, pediatric lupus, non-renal lupus,extra-renal lupus, discoid lupus and discoid lupus erythematosus,alopecia lupus, SLE, such as cutaneous SLE or subacute cutaneous SLE,neonatal lupus syndrome (NLE), and lupus erythematosus disseminatus,juvenile onset (Type I) diabetes mellitus, including pediatric IDDM,adult onset diabetes mellitus (Type II diabetes), autoimmune diabetes,idiopathic diabetes insipidus, diabetic retinopathy, diabeticnephropathy, diabetic colitis, diabetic large-artery disorder, immuneresponses associated with acute and delayed hypersensitivity mediated bycytokines and T-lymphocytes, tuberculosis, sarcoidosis, granulomatosisincluding lymphomatoid granulomatosis, agranulocytosis, vasculitides(including large-vessel vasculitis such as polymyalgia rheumatica andgiant-cell (Takayasu's) arteritis, medium-vessel vasculitis such asKawasaki's disease and polyarteritis nodosa/periarteritis nodosa,immunovasculitis, CNS vasculitis, cutaneous vasculitis, hypersensitivityvasculitis, necrotizing vasculitis such as fibrinoid necrotizingvasculitis and systemic necrotizing vasculitis, ANCA-negativevasculitis, and ANCA-associated vasculitis such as Churg-Strausssyndrome (CSS), Wegener's granulomatosis, and microscopic polyangiitis),temporal arteritis, aplastic anemia, autoimmune aplastic anemia, Coombspositive anemia, Diamond Blackfan anemia, hemolytic anemia or immunehemolytic anemia including autoimmune hemolytic anemia (AIHA),pernicious anemia (anemia perniciosa), Addison's disease, pure red cellanemia or aplasia (PRCA), Factor VIII deficiency, hemophilia A,autoimmune neutropenia(s), cytopenias such as pancytopenia, leukopenia,diseases involving leukocyte diapedesis, CNS inflammatory disorders,Alzheimer's disease, Parkinson's disease, multiple organ injury syndromesuch as those secondary to septicemia, trauma or hemorrhage,antigen-antibody complex-mediated diseases, anti-glomerular basementmembrane disease, anti-phospholipid antibody syndrome, motoneuritis,allergic neuritis, Behcet's disease/syndrome, Castleman's syndrome,Goodpasture's syndrome, Reynaud's syndrome, Sjögren's syndrome,Stevens-Johnson syndrome, pemphigoid or pemphigus such as pemphigoidbullous, cicatricial (mucous membrane) pemphigoid, skin pemphigoid,pemphigus vulgaris, paraneoplastic pemphigus, pemphigus foliaceus,pemphigus mucus-membrane pemphigoid, and pemphigus erythematosus,epidermolysis bullosa acquisita, ocular inflammation, including allergicocular inflammation such as allergic conjunctivis, linear IgA bullousdisease, autoimmune-induced conjunctival inflammation, autoimmunepolyendocrinopathies, Reiter's disease or syndrome, thermal injury dueto an autoimmune condition, preeclampsia, an immune complex disordersuch as immune complex nephritis, antibody-mediated nephritis,neuroinflammatory disorders, polyneuropathies, chronic neuropathy suchas IgM polyneuropathies or IgM-mediated neuropathy, thrombocytopenia (asdeveloped by myocardial infarction patients, for example), includingthrombotic thrombocytopenic purpura (TTP), post-transfusion purpura(PTP), heparin-induced thrombocytopenia, and autoimmune orimmune-mediated thrombocytopenia including, for example, idiopathicthrombocytopenic purpura (ITP) including chronic or acute ITP, scleritissuch as idiopathic cerato-scleritis, episcleritis, autoimmune disease ofthe testis and ovary including autoimmune orchitis and oophoritis,primary hypothyroidism, hypoparathyroidism, autoimmune endocrinediseases including thyroiditis such as autoimmune thyroiditis,Hashimoto's disease, chronic thyroiditis (Hashimoto's thyroiditis), orsubacute thyroiditis, autoimmune thyroid disease, idiopathichypothyroidism, Grave's disease, Grave's eye disease (ophthalmopathy orthyroid-associated ophthalmopathy), polyglandular syndromes such asautoimmune polyglandular syndromes, for example, type I (orpolyglandular endocrinopathy syndromes), paraneoplastic syndromes,including neurologic paraneoplastic syndromes such as Lambert-Eatonmyasthenic syndrome or Eaton-Lambert syndrome, stiff-man or stiff-personsyndrome, encephalomyelitis such as allergic encephalomyelitis orencephalomyelitis allergica and experimental allergic encephalomyelitis(EAE), myasthenia gravis such as thymoma-associated myasthenia gravis,cerebellar degeneration, neuromyotonia, opsoclonus or opsoclonusmyoclonus syndrome (OMS), and sensory neuropathy, multifocal motorneuropathy, Sheehan's syndrome, autoimmune hepatitis, chronic hepatitis,lupoid hepatitis, giant-cell hepatitis, chronic active hepatitis orautoimmune chronic active hepatitis, pneumonitis such as lymphoidinterstitial pneumonitis (LIP), bronchiolitis obliterans(non-transplant) vs. NSIP, Guillain-Barré syndrome, Berger's disease(IgA nephropathy), idiopathic IgA nephropathy, linear IgA dermatosis,acute febrile neutrophilic dermatosis, subcorneal pustular dermatosis,transient acantholytic dermatosis, cirrhosis such as primary biliarycirrhosis and pneumonocirrhosis, autoimmune enteropathy syndrome, Celiacor Coeliac disease, celiac sprue (gluten enteropathy), refractory sprue,idiopathic sprue, cryoglobulinemia such as mixed cryoglobulinemia,amylotrophic lateral sclerosis (ALS; Lou Gehrig's disease), coronaryartery disease, autoimmune ear disease such as autoimmune inner eardisease (AIED), autoimmune hearing loss, polychondritis such asrefractory or relapsed or relapsing polychondritis, pulmonary alveolarproteinosis, keratitis such as Cogan's syndrome/nonsyphiliticinterstitial keratitis, Bell's palsy, Sweet's disease/syndrome, rosaceaautoimmune, zoster-associated pain, amyloidosis, a non-cancerouslymphocytosis, a primary lymphocytosis, which includes monoclonal B celllymphocytosis (e.g., benign monoclonal gammopathy and monoclonalgammopathy of undetermined significance, MGUS), peripheral neuropathy,paraneoplastic syndrome, channelopathies such as epilepsy, migraine,arrhythmia, muscular disorders, deafness, blindness, periodic paralysis,and channelopathies of the CNS, autism, inflammatory myopathy, focal orsegmental or focal segmental glomerulosclerosis (FSGS), endocrineophthalmopathy, uveoretinitis, chorioretinitis, autoimmune hepatologicaldisorder, fibromyalgia, multiple endocrine failure, Schmidt's syndrome,adrenalitis, gastric atrophy, presenile dementia, demyelinating diseasessuch as autoimmune demyelinating diseases and chronic inflammatorydemyelinating polyneuropathy, Dressler's syndrome, alopecia greata,alopecia totalis, CREST syndrome (calcinosis, Raynaud's phenomenon,esophageal dysmotility, sclerodactyl), and telangiectasia), male andfemale autoimmune infertility, e.g., due to anti-spermatozoanantibodies, mixed connective tissue disease, Chagas' disease, rheumaticfever, recurrent abortion, farmer's lung, erythema multiforme,post-cardiotomy syndrome, Cushing's syndrome, bird-fancier's lung,allergic granulomatous angiitis, benign lymphocytic angiitis, Alport'ssyndrome, alveolitis such as allergic alveolitis and fibrosingalveolitis, interstitial lung disease, transfusion reaction, leprosy,malaria, parasitic diseases such as leishmaniasis, trypanosomiasis,schistosomiasis, ascariasis, aspergillosis, Sampter's syndrome, Caplan'ssyndrome, dengue, endocarditis, endomyocardial fibrosis, diffuseinterstitial pulmonary fibrosis, interstitial lung fibrosis, fibrosingmediastinitis, pulmonary fibrosis, idiopathic pulmonary fibrosis, cysticfibrosis, endophthalmitis, erythema elevatum et diutinum,erythroblastosis fetalis, eosinophilic faciitis, Shulman's syndrome,Felty's syndrome, flariasis, cyclitis such as chronic cyclitis,heterochronic cyclitis, iridocyclitis (acute or chronic), or Fuch'scyclitis, Henoch-Schonlein purpura, human immunodeficiency virus (HIV)infection, SOD, acquired immune deficiency syndrome (AIDS), echovirusinfection, sepsis (systemic inflammatory response syndrome (SIRS)),endotoxemia, pancreatitis, thyroxicosis, parvovirus infection, rubellavirus infection, post-vaccination syndromes, congenital rubellainfection, Epstein-Barr virus infection, mumps, Evan's syndrome,autoimmune gonadal failure, Sydenham's chorea, post-streptococcalnephritis, thromboangitis ubiterans, thyrotoxicosis, tabes dorsalis,chorioiditis, giant-cell polymyalgia, chronic hypersensitivitypneumonitis, conjunctivitis, such as vernal catarrh,keratoconjunctivitis sicca, and epidemic keratoconjunctivitis,idiopathic nephritic syndrome, minimal change nephropathy, benignfamilial and ischemia-reperfusion injury, transplant organ reperfusion,retinal autoimmunity, joint inflammation, bronchitis, chronicobstructive airway/pulmonary disease, silicosis, aphthae, aphthousstomatitis, arteriosclerotic disorders (cerebral vascular insufficiency)such as arteriosclerotic encephalopathy and arterioscleroticretinopathy, aspermiogenese, autoimmune hemolysis, Boeck's disease,cryoglobulinemia, Dupuytren's contracture, endophthalmiaphacoanaphylactica, enteritis allergica, erythema nodosum leprosum,idiopathic facial paralysis, chronic fatigue syndrome, febrisrheumatica, Hamman-Rich's disease, sensoneural hearing loss,haemoglobinuria paroxysmatica, hypogonadism, ileitis regionalis,leucopenia, mononucleosis infectiosa, traverse myelitis, primaryidiopathic myxedema, nephrosis, ophthalmia symphatica (sympatheticophthalmitis), neonatal ophthalmitis, optic neuritis, orchitisgranulomatosa, pancreatitis, polyradiculitis acuta, pyodermagangrenosum, Quervain's thyreoiditis, acquired spenic atrophy,non-malignant thymoma, lymphofollicular thymitis, vitiligo, toxic-shocksyndrome, food poisoning, conditions involving infiltration of T cells,leukocyte-adhesion deficiency, immune responses associated with acuteand delayed hypersensitivity mediated by cytokines and T-lymphocytes,diseases involving leukocyte diapedesis, multiple organ injury syndrome,antigen-antibody complex-mediated diseases, antiglomerular basementmembrane disease, autoimmune polyendocrinopathies, oophoritis, primarymyxedema, autoimmune atrophic gastritis, rheumatic diseases, mixedconnective tissue disease, nephrotic syndrome, insulitis, polyendocrinefailure, autoimmune polyglandular syndromes, including polyglandularsyndrome type I, adult-onset idiopathic hypoparathyroidism (AOIH),cardiomyopathy such as dilated cardiomyopathy, epidermolisis bullosaacquisita (EBA), hemochromatosis, myocarditis, nephrotic syndrome,primary sclerosing cholangitis, purulent or nonpurulent sinusitis, acuteor chronic sinusitis, ethmoid, frontal, maxillary, or sphenoidsinusitis, allergic sinusitis, an eosinophil-related disorder such aseosinophilia, pulmonary infiltration eosinophilia, eosinophilia-myalgiasyndrome, Loffler's syndrome, chronic eosinophilic pneumonia, tropicalpulmonary eosinophilia, bronchopneumonic aspergillosis, aspergilloma, orgranulomas containing eosinophils, anaphylaxis, spondyloarthropathies,seronegative spondyloarthritides, polyendocrine autoimmune disease,sclerosing cholangitis, sclera, episclera, chronic mucocutaneouscandidiasis, Bruton's syndrome, transient hypogammaglobulinemia ofinfancy, Wiskott-Aldrich syndrome, ataxia telangiectasia syndrome,angiectasis, autoimmune disorders associated with collagen disease,rheumatism such as chronic arthrorheumatism, lymphadenitis, reduction inblood pressure response, vascular dysfunction, tissue injury,cardiovascular ischemia, hyperalgesia, renal ischemia, cerebralischemia, and disease accompanying vascularization, allergichypersensitivity disorders, glomerulonephritides, reperfusion injury,ischemic re-perfusion disorder, reperfusion injury of myocardial orother tissues, lymphomatous tracheobronchitis, inflammatory dermatoses,dermatoses with acute inflammatory components, multiple organ failure,bullous diseases, renal cortical necrosis, acute purulent meningitis orother central nervous system inflammatory disorders, ocular and orbitalinflammatory disorders, granulocyte transfusion-associated syndromes,cytokine-induced toxicity, narcolepsy, acute serious inflammation,chronic intractable inflammation, pyelitis, endarterial hyperplasia,peptic ulcer, valvulitis, and endometriosis.

General Techniques

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques of molecular biology (includingrecombinant techniques), microbiology, cell biology, biochemistry, andimmunology, which are within the skill of the art. Such techniques areexplained fully in the literature, such as, “Molecular Cloning: ALaboratory Manual”, second edition (Sambrook et al., 1989);“Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal CellCulture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (AcademicPress, Inc.); “Current Protocols in Molecular Biology” (F. M. Ausubel etal., eds., 1987, and periodic updates); “PCR: The Polymerase ChainReaction”, (Mullis et al., eds., 1994).

Primers, oligonucleotides and polynucleotides employed in the presentinvention can be generated using standard techniques known in the art.

Gene expression signatures and biomarkers associated with predictingresponsiveness of RA patients and patients suffering with otherautoimmune diseases such as MS and ANCA-vasculitis to certaintherapeutic agents are provided herein. These signatures as well asexpression levels of the mRNA or individual proteins encoded by thegenes constitute biomarkers for predicting responsiveness to RAtherapeutic agents, MS therapeutic agents, and/or ANCA-vasculitistherapeutic agents. Accordingly, the invention disclosed herein isuseful in a variety of settings, e.g., in methods and compositionsrelated to diagnosis and therapy of autoimmune diseases.

Detection of Gene Expression Levels

Nucleic acid, according to any of the methods described herein may beRNA transcribed from genomic DNA or cDNA generated from RNA or mRNA.Nucleic acid may be derived from a vertebrate, e.g., a mammal. A nucleicacid is said to be “derived from” a particular source if it is obtaineddirectly from that source or if it is a copy of a nucleic acid found inthat source.

Nucleic acid includes copies of the nucleic acid, e.g., copies thatresult from amplification. Amplification may be desirable in certaininstances, e.g., in order to obtain a desired amount of material fordetecting variations. The amplicons may then be subjected to a variationdetection method, such as those described below, to determine expressionof certain genes.

Levels of mRNA may be measured and quantified by various methodswell-known to those skilled in the art, including use of commerciallyavailable kits and reagents. One such method is polymerase chainreaction (PCR). Another method, for quantitative use, is real-timequantitative PCR, or qPCR. See, e.g., “PCR Protocols, A Guide to Methodsand Applications,” (M. A. Innis et al., eds., Academic Press, Inc.,1990); “Current Protocols in Molecular Biology” (F. M. Ausubel et al.,eds., 1987, and periodic updates); and “PCR: The Polymerase ChainReaction”, (Mullis et al., eds., 1994).

A microarray is a multiplex technology that typically uses an arrayedseries of thousands of nucleic acid probes to hybridize with, e.g, acDNA or cRNA sample under high-stringency conditions. Probe-targethybridization is typically detected and quantified by detection offluorophore-, silver-, or chemiluminescence-labeled targets to determinerelative abundance of nucleic acid sequences in the target. In typicalmicroarrays, the probes are attached to a solid surface by a covalentbond to a chemical matrix (via epoxy-silane, amino-silane, lysine,polyacrylamide or others). The solid surface is for example, glass, asilicon chip, or microscopic beads. Various microarrays are commerciallyavailable, including those manufactured, for example, by Affymetrix,Inc. and Illumina, Inc.

A biological sample may be obtained using certain methods known to thoseskilled in the art. Biological samples may be obtained from vertebrateanimals, and in particular, mammals. In certain instances, a biologicalsample is synovial tissue, serum or peripheral blood mononuclear cells(PBMC). By screening such body samples, a simple early diagnosis can beachieved for diseases such as RA, MS, or ANCA-vasculitis. In addition,the progress of therapy can be monitored more easily by testing suchbody samples for variations in expression levels of target nucleic acids(or encoded polypeptides).

Subsequent to the determination that a subject, or the tissue or cellsample comprises a gene expression signature or relative levels ofcertain serum biomarkers disclosed herein, it is contemplated that aneffective amount of an appropriate therapeutic agent may be administeredto the subject to treat the particular disease in the subject, e.g., RA,MS, or ANCA-vasculitis. Clinical diagnosis in mammals of the variouspathological conditions described herein can be made by the skilledpractitioner. Clinical diagnostic techniques are available in the artwhich allow, e.g., for the diagnosis or detection of autoimmune diseasesin a mammal, e.g., RA, MS, or ANCA-vasculitis.

A therapeutic agent can be administered in accordance with knownmethods, such as intravenous administration as a bolus or by continuousinfusion over a period of time, by intramuscular, intraperitoneal,intracerobrospinal, subcutaneous, intra-articular, intrasynovial,intrathecal, oral, topical, or inhalation routes. Optionally,administration may be performed through mini-pump infusion using variouscommercially available devices.

Kits

For use in the applications described or suggested herein, kits orarticles of manufacture are also provided. Such kits may comprise acarrier means being compartmentalized to receive in close confinementone or more container means such as vials, tubes, and the like, each ofthe container means comprising one of the separate elements to be usedin the method. For example, one of the container means may comprise aprobe that is or can be detectably labeled. Such probe may be apolynucleotide specific for a polynucleotide comprising one or moregenes of a gene expression signature. Where the kit utilizes nucleicacid hybridization to detect the target nucleic acid, the kit may alsohave containers containing nucleotide(s) for amplification of the targetnucleic acid sequence and/or a container comprising a reporter means,such as a biotin-binding protein, such as avidin or streptavidin, boundto a reporter molecule, such as an enzymatic, florescent, orradioisotope label.

Kits will typically comprise the container described above and one ormore other containers comprising materials desirable from a commercialand user standpoint, including buffers, diluents, filters, needles,syringes, and package inserts with instructions for use. A label may bepresent on the container to indicate that the composition is used for aspecific therapy or non-therapeutic application, and may also indicatedirections for either in vivo or in vitro use, such as those describedabove. Other optional components in the kit include one or more buffers(e.g., block buffer, wash buffer, substrate buffer, etc), other reagentssuch as substrate (e.g., chromogen) which is chemically altered by anenzymatic label, epitope retrieval solution, control samples (positiveand/or negative controls), control slide(s) etc.

Methods of Marketing

The invention herein also encompasses a method for marketing atherapeutic agent or a pharmaceutically acceptable composition thereofcomprising promoting to, instructing, and/or specifying to a targetaudience, the use of the agent or pharmaceutical composition thereof fortreating a patient or patient population with a particular disease,e.g., RA, MS, or ANCA-vasculitis, from which a sample has been obtainedshowing a gene expression signature or levels of serum biomarkers asdisclosed herein.

Marketing is generally paid communication through a non-personal mediumin which the sponsor is identified and the message is controlled.Marketing for purposes herein includes publicity, public relations,product placement, sponsorship, underwriting, and sales promotion. Thisterm also includes sponsored informational public notices appearing inany of the print communications media designed to appeal to a massaudience to persuade, inform, promote, motivate, or otherwise modifybehavior toward a favorable pattern of purchasing, supporting, orapproving the invention herein.

The marketing of the diagnostic method herein may be accomplished by anymeans. Examples of marketing media used to deliver these messagesinclude television, radio, movies, magazines, newspapers, the internet,and billboards, including commercials, which are messages appearing inthe broadcast media.

The type of marketing used will depend on many factors, for example, onthe nature of the target audience to be reached, e.g., hospitals,insurance companies, clinics, doctors, nurses, and patients, as well ascost considerations and the relevant jurisdictional laws and regulationsgoverning marketing of medicaments and diagnostics. The marketing may beindividualized or customized based on user characterizations defined byservice interaction and/or other data such as user demographics andgeographical location.

EXAMPLES

The following are examples of the methods and compositions of theinvention. It is understood that various other embodiments may bepracticed, given the general description provided above.

Example 1 Introduction

Randomized and placebo controlled clinical trials have shown thatrituximab is efficacious for. RA patients who have failed methotrexate(MTX) and/or anti-TNF therapy (Emery P, et al., Arthritis Rheum. 2006;54 (5):1390-400; Cohen S B, et al., Arthritis Rheum. 2006; 54 (9):2793-806). Similar to other immunology biologics, rituximab isassociated with certain risks such as infusion reactions and infection,among other possible side effects. To improve the benefit/risk equationfor rituximab therapy in RA, we have been interested in identifyingbaseline predictive clinical features or molecular biomarkers thatidentify patient subpopulations with an increased response rate.Similarly, there is interest in identifying patient subsets that receiveno benefit from rituximab so that alternative therapies can beprescribed. A recent study suggests that elevated levels ofautoantibodies (rheumatoid factor and/or anti-CCP antibodies) and theacute phase reactant C-reactive protein enrich for responders torituximab in RA (Sellam et al., Arthritis & Rheumatism 2011; 63:93-938;Domer et al., Pharmacol Ther 2010; 125:464-475).

The aims of the current study were to validate an mRNA-based methodologyto quantitate the levels of B lineage cells in peripheral blood, andthen determine whether differences in B cell subset composition prior totherapy correlated with clinical response to rituximab in RA. The datasupport the concept that elevated baseline blood levels of molecularmarkers for late B lineage stage plasmablasts are predictive ofnon-response to anti-CD20 therapy in RA.

Methods and Subjects Clinical Study Designs and Sample Collection

REFLEX was a multicenter, randomized, double-blind, placebo-controlled,phase III clinical study of rituximab (2×1000 mg) treatment in 518patients with active RA and an inadequate response to 1 or more anti-TNFagents (TNF-IR) (Cohen S B, et al., Arthritis Rheum. 2006; 54 (9):2793-806). DANCER was a randomized, multicenter, double-blind,placebo-controlled phase II clinical trial that enrolled 462 RApatients. Subjects were randomized to receive placebo, rituximab 2×500mg, or rituximab 2×1000 mg, with or without glucocorticoids. A completecharacterization of patient demographics, baseline clinical features andoutcomes from the DANCER trial has been published (Emery P, et al.,Arthritis Rheum. 2006; 54 (5):1390-400.). SERENE was a phase IIIrandomized placebo-controlled trial to assess efficacy of two doseregimens of rituximab (2×500 mg and 2×1000 mg) in 512 RA patients withan inadequate response to methotrexate (MTX-IR) (Emery P, et al., AnnRheum Dis. 2010 September; 69(9):1629-35. Epub 2010 May 20). Inclusioncriteria for the three trials included: diagnosis of rheumatoidarthritis according to the revised American College of Rheumatologycriteria at least 6 months prior to enrollment, age between 18-80 years,swollen joint counts≧8 (66 joint count) and tender joint counts≧8 (68joint count) at time of screening at baseline and screening, eitherESR≧28 mm/hr or CRP≧1.5 mg/dL (REFLEX, DANCER) or ESR≧28 mm/hr orCRP≧0.6 mg/dL (SERENE) at time of screening, and receiving MTX at a dose10-25 mg/week for at least 12 weeks with the last 4 weeks at a stabledose. Additional requirements for REFLEX included a wash out period frometanercept for ≧4 weeks and Infliximab for ≧8 weeks and radiographicevidence of erosion in at least one joint. In all three trials,rituximab or placebo were administered by intravenous infusion on daysone and 15 with concomitant methotrexate (10-25 mg/week as prescribed bythe treating physician). In all patients, 100 mg intravenous infusionmethylprednisolone was administered at least 30 minutes prior torituximab or placebo infusion. All patients also received 5 mg/weekfolate.

SCRIPT was a multicenter, randomized, double-blind, placebo-controlledphase III clinical trial of ocrelizumab, a humanized anti-CD20monoclonal antibody, in 840 TNF-IR RA patients. Patients were on aconcomitant background of non-biologic DMARD therapy. Subjects wererandomized into three trial arms and received 2 courses of placebo or200 mg or 500 mg of ocrelizumab and were assessed for clinical benefitthroughout 48 weeks after dosing. Inclusion criteria for the trialincluded RA diagnosis for at least 3 months using the 1987 ACR criteriafor classification of RA, swollen joint count (66 joints)≧4, tenderjoint count (68 joints)≧4, CRP≧0.6 mg/dL and positive rheumatoid factorand/or anti-CCP antibody status.

Baseline demographics and clinical activity measures for each of thetrial populations are summarized in Tables 2 and 3 below.

For development of the mRNA-based biomarkers (see below) we used samplesfrom the ACTION trial. ACTION was a combined phase I/II dose-rangingstudy of MTX plus placebo versus MTX and ocrelizumab in RA patients.Complete patient demographics, clinical findings and outcomes for theACTION trial have been published (Genovese M C, et al, Arthritis Rheum.2008 September; 58(9):2652-61). Whole blood PaxGene samples for RT-qPCRand microarray gene expression analysis as well as EDTA blood for FACSanalysis were obtained at baseline and pre-defined timepoints on allpatients enrolled in the study.

Baseline PaxGene blood RNA sample collection in all of the anti-CD20trials was optional and obtained following informed consent. Thus, RNAsamples were available from a subset only of each trial population (27%,31%, 30% and 49% of samples from REFLEX, DANCER, SERENE and SCRIPT,respectively).

Methods Microarray Methods and Analysis

RNA was purified at Covance (Princeton, N.J.) using the manufacturer'srecommended protocol and reagents (PAXgene™ blood RNA kit, Qiagen Inc,Valencia, Calif.). The amount and quality of RNA extracted were assessedwith NanoDrop (ND1000, Celbio, Mich.) and Agilent 2100 Bioanalyzer(Agilent Technologies Inc, Headquarters Santa Clara, Calif.).

RNA from a subset of 24 study patients was profiled on Agilent WholeHuman Genome 4×44 microarrays (Part ID G4112-60510, Agilent TechnologiesInc, Headquarters Santa Clara, Calif.). Microarray images were analyzedusing Agilent's Feature Extraction (FE) software, version 9.5.Differential gene expression analysis was performed using Parteksoftware (Partek Inc., St. Louis, Mo.). In brief, gene expression datawas log-transformed and quantile normalized. A list of mostsignificantly different genes based on fold-change and p-values betweendepleters and non-depleters (as determined by FACS analysis) at baselineand at day 84 post riuximab (RTX) treatment was derived using a 3 wayANOVA. The initial list constituted mainly of immunoglobulin chaingenes, as well as established plasma cell markers and B cell markers.From the top ˜30 genes, 7 genes were chosen for further analysis, basedon their performance, specificity, and preliminary in vitro experiments(data not shown).

Gene Expression Analysis Reagents and Instrumentation

TaqMan Universal Master Mix, TaqMan PreAmp Master Mix and geneexpression assays were from Applied Biosystems (Applied Biosystems,Foster City, Calif.). Pre-amplification reactions were performed using aGeneAmp PCR System 9700 (Applied Biosystems). Real-time PCR reactionswere performed using either the Fluidigm digital array gene expressiontechnology (Fluidigm Corporation, South San Francisco, Calif.) or in 384well plates utilizing the ABI Prism 7900HT instrument (AppliedBiosystems, Foster City, Calif.). Both real-time PCR methods werevalidated against each other in a series of QC experiments (data notshown).

Candidate mRNA Biomarker Selection

The following B cell genes were initially selected for multiplex RT-qPCRgene

expression analysis: 1) genes enriched in naïve and memory B cells(CD19, CD20, POU2AF1, FCRL5 splice variant—FCRL5/IRTA2c, inventoried ABIassay HS01070204_ml, shown in preliminary experiments to be expressedpredominantly on naïve and mature B cells, as opposed to IRTA 2a and bwhich are expressed predominantly in bone marrow plasma cells (Polson AG, et al., Int Immunol. 2006 September; 18(9):1363-73. Epub 2006 Jul.18); 2) genes enriched in plasmablasts/plasma cells (Ig-J chain, BCMA);and 3) genes found in both B cells and (at higher levels in) plasmacells (Ig light chain). POU2AF1 did not perform well likely due its lowabundance, and IgL did not discriminate mature B cells from plasmablastsin our hands; thus, these two markers were not considered further. Alldata were normalized for the housekeeping gene GAPDH. All primer/probesets were TaqMan Gene Expression Assays (Applied Biosystems, FosterCity, Calif.).

RNA, cDNA and qPCR

RNA was extracted from whole blood using PAXgene™ blood RNA kits,according to manufacturer's protocol (Qiagen Inc, Valencia, Calif.). Theamount and quality of RNA extracted were assessed using both NanoDrop(ND 1000, Celbio, Mich.) and Agilent 2100 Bioanalyzer (AgilentTechnologies Inc, Santa Clara, Calif.) technologies.

In the initial step of the qPCR multiplex assay, 100 ng RNA per samplewas reversed transcribed to cDNA using BioRad iScript cDNA Synthesis kit(BioRad, Hercules, Calif.) except that for the SCRIPT samples, 300 ngRNA was used and, after synthesis, diluted with water to 10 ng/ul inputRNA. Subsequently, a preliminary cDNA amplification step employingspecific primer pairs was performed using a commercially available cDNApreamplification kit (TaqMan PreAmp Master Mix Kit, Applied Biosystems),as previously described (Ciotti P, et al., Diagn Mol. Pathol. 2009 June;18(2):112-8). Preamplification product was diluted 1:5 with TE bufferaccording to the manufacturer's protocol. Samples from the SCRIPT trialwere not preamplified. Quantitative PCR was performed using either theFluidigm digital array gene expression technology (Fluidigm Corporation,South San Francisco, Calif.) or the ABI 7900HT instrument (AppliedBiosystems, Foster City, Calif.). For the Fluidigm dynamic arrays, 2.25ul preamplified cDNA per reaction was used and for the Taqman assays, 2ul of preamplified or non-amplified cDNA (SCRIPT) was used per reaction.

To assess potential biases between pre-amplified and non-amplifiedproduct in the qPCR reactions, a range of preamplified (50 ng to 5 ng)and non-amplified RNA templates from human B cell lines and tonsil RNAwere tested. Expression of each gene was measured in duplicate in eachexperiment, and the average of the replicates was normalized to humanGAPDH to generate a delta Ct (ΔCt) value for each gene. Duplicatesamples generally varied by no more than 5%. Data was analyzed usingBioMark Gene Expression Data Analysis software (Fluidigm Corporation,South San Francisco, Calif.) to obtain Ct values. Expression data wasthen calculated as relative abundance, using the formula 2^(−ΔCt).

Assessment of Gene Expression in B Cell Lineages

Human B cells were sorted from peripheral blood or leukopacks fromhealthy donors using markers to distinguish between naïve B cells,unswitched and switched memory B cells and plasma cells as previouslydescribed (Abbas et al., Genes Immun 2005; 6: 319-331). Naïve B cellswere CD19+CD27−IgG/A−, unswitched memory B cells were CD19+CD27+IgG/A−,and switched memory B cells were CD19+CD27+IgM−. Plasma cells wereCD19+CD138+. RNA was purified and hybridized to Affymetrix® HGU133A andHGU133B GeneChips®. Mean probe expression levels for IgJ, FcRL5/IRTA2c,CD19 and BCMA were determined from the respective normalizedfluorescence values for each B cell population.

Statistical Analyses

Select clinical case report form data was transferred from clinicaltrial databases at Genentech into a customized Oracle database designedto facilitate biomarker discovery. Data analysis was performed using JMPsoftware (SAS, Cary, N.C.), and all statistical analysis was performedusing GraphPad Prism software (GraphPad, La Jolla, Calif.).

Differences in expression between ACR50 responders vs. non-responders inthe active and placebo arms with respect to the linearly transformedvalues were assessed using the nonparametric Mann-Whitney test.

A threshold sensitivity method was applied to baseline RNA samples fromthe REFLEX trial in order to identify candidate biomarker thresholdsthat enriched for placebo corrected lack of response as defined byfailure to achieve ACR50 at 24 weeks. The threshold sensitivity methodand analysis were carried out as follows.

To identify subgroups with increased clinical benefit, the studypopulation from REFLEX was stratified using baseline clinicalcharacteristics and serological biomarkers measured in patients for whomserum samples were available. The baseline characteristics for thepatient subgroups that had matching biomarker serum samples werecomparable with the overall patient group in the clinical trial. Forsurveys of each continuous biomarker (where a range of discrete valueswas possible) and outcome measure ACR50 at week 24, a plot was generatedpresenting subgroup efficacy differentials versus a range of potentialthreshold values (20th-80th biomarker percentiles in 5-percentileincrements) to control bias. The threshold giving the largest efficacydifferential (Δhigh-Δlow) was then identified. For this threshold, apermutation test was used to address statistical significance. For eachpermutation, biomarker values were permuted and both treatmentassignment and the outcome measure were fixed. The largest efficacydifferential was computed for the permutated data set, which wascompared to the largest efficacy differential observed from the originaldata. Permutation p-values were based on 2000 permutations. A 95%confidence interval on the largest efficacy differential was calculated.Four biomarkers with the highest efficacy differentials (CRP,IgG-anti-CCP, IgA-RF and sCD25) that identified subgroups in REFLEX withenhanced clinical benefit in rituximab-treated patients were thenprioritized and further investigated in the SERENE trial dataset. Inaddition, five of their two-biomarker (bivariate) combinations were alsostudied. The sixth combination, IgG- anti-CCP and IgA-RF, was notconsidered due to a high correlation between the two markers. BecauseCRP is one of the components of the ACR efficacy measure, also DAS-ESRwas prioritized for testing in the SERENE data set.

Recently, it was reported that there were no significant differences ineither clinical or safety outcomes between rituximab doses in the SERENEtrial (500 mg and 1000 mg) (Emery P, et al., Ann Rheum Dis. 2010September; 69(9):1629-35. Epub 2010 May 20). Because ACR50 responserates were similar between the rituximab 500-mg (26.3%; n=167) andrituximab 1000-mg (25.9%; n=170) dose groups at 24 weeks in SERENE andpharmacodynamic properties were comparable between the two doses (EmeryP, et al., Arthritis Rheum. 2006; 54 (5):1390-400), we combined bothdoses as a single treatment group for this analysis. Each biomarker wasanalyzed as described for REFLEX. Each of five bivariate subgroupcandidates was constructed using an “and” rule and applying the samedirection (i.e. high or low) that defined the best subgroup for theindividual biomarkers. Bivariate subgroup candidates were formed bycomparing patients with both elevated CRP and elevated IgA RF topatients who were not in this subgroup; subgroups were determined by30th, 40th, 50th, 60th and 70th percentiles of either CRP or IgA-RF withthe constraint that at least 20% of the patients were in each subgroupto control bias. Exploratory analyses of other non-prioritized baselinebiomarkers (e.g. IgM-RF, IgG-RF, and IgG-anti-CCP) and combinations ofbiomarkers were also performed.

The thresholds for the predictive biomarkers and two-biomarkercombinations once established in the REFLEX trial were thenprospectively tested following a pre-specified diagnostic plan usingdata from the replication cohort, which was comprised of samplescombined from the SERENE and DANCER trials.

For SCRIPT, due to our use of non-amplified RNA, we prospectivelyapplied the overall percentage thresholds derived from the active armsamples from the three rituximab studies in the analysis. Thus forSCRIPT, IgJ^(hi) was defined as the top 20% of samples (FIG. 6), andFCRL5^(lo) was defined as the bottom 15% of samples. The prospectivelydefined cutoff of the highest 20th percentile of IgJ abundance used todetermine IgJ^(hi) biomarker status in SCRIPT is indicated by the dottedline in FIG. 6. Individual with IgJ levels above the 20% threshold areshown as open squares.

Differences in ACR20, ACR50, ACR70, ACRn, and DAS28 responses betweenactive and placebo arms for the biomarker positive and negative patientsubsets in the test and replication cohorts were calculated, andP-values determined. For categorical variables (ACR20, ACR50, ACR70) twoseparate contingency tables, one for the active arm and one for theplacebo arm, were created for each cohort (test, replication and all) tocompare the proportion of responders in the biomarker positive vs.biomarker negative subsets. Statistical significance was calculatedusing Fisher's exact test, and 2-tailed P-values were calculated. Oddsratios and inferential statistical calculations were performed using theR Language for Statistical Computing. Confidence intervals for oddsratios were based on the two-tailed Fisher's Exact test. P-values forDAS28 scores were derived from the two-tailed Student's t-test.Correlation coefficients were calculated using Pearson correlationcoefficients. Clustering was performed using Treeview software (Page, R.D. M., Computer Applications in the Biosciences 1996 12: 357-358.).

Results RT-qPCR mRNA Assays for B Lineage Cells in Whole Blood

We first set out to develop an mRNA-based method to detect and quantifyB cells in whole blood. Multiplex reverse transcriptase-quantitativePCR(RT-qPCR) analysis was performed on whole blood RNA samples frompatients receiving B cell depletion (rituximab or ocrelizumab) therapy,including samples from pre-therapy baseline, and days 15 and 84 post-Bcell depletion. RT-qPCR assays were designed for CD19, CD20 and a B cellspecific splice variant of FCRL5/IRTA2c, all markers of mature B cells.Additional assays were designed for J-chain (IgJ) and BCMA, genes highlyenriched in B plasmablasts and plasma cells. Flow cytometry wasperformed at baseline and days 15 and 84 post-therapy, and Agilent geneexpression microarray data were generated for a subset of the samples(baseline and day 84) (see Methods above).

We found high-level concordance between B cell gene expression levels asdetermined by CD20 mRNA RT-qPCR analysis and absolute CD 19+ cell countsas determined by flow cytometry (r²=0.52, P<0.0001) (FIG. 1A). For theexperiment shown in FIG. 1A, CD19 positive B cells in blood (cells/4 μl;y axis) were quantitated using flow cytometry in a total of 186 samplescollected at various timepoints from patients undergoing anti-CD20 Bcell depletion therapy. Whole blood RNAs sampled at the same time wereassayed for CD20 expression levels (x axis) using RT-qPCR (see Methodsabove), and a Pearson correlation coefficient was calculated.Importantly, the RT-qPCR method retained high sensitivity at low B celllevels. Using multivariate correlation plots and unsupervisedclustering, the 5 tested genes partitioned into two independent markersets (FIG. 1B). For the results shown in FIG. 1B, correlationcoefficients were calculated between RT-qPCR mRNA expression levels ofplasmablasts (IgJ and BCMA) and mature B cell markers (FCRL5, CD19 andCD20) and various B cell subsets as determined by flow cytometry, andthen visualized using unsupervised clustering. Expression of CD19, CD20and FCRL5 correlated with each other (r>0.75) and with absolute CD 19+and CD27− naïve B cell counts (r>0.45). IgJ and BCMA were correlatedwith each other (r>0.8), but were poorly correlated with CD 19+, CD27−naïve or CD27+ memory B cell counts. The two mRNA marker groups showedonly low-level correlation with each other (r<0.4) (FIG. 1B and Table1).

TABLE 1 Correlation coefficients for RT-qPCR mRNA levels betweenplasmablast/plasma cell markers (BCMA, IgJ) and mature/ memory B cellmarkers (CD19, CD20, FCRL5). BCMA IgJ CD19 CD20 FCRL5 BCMA 1.00 0.870.38 0.42 0.40 IgJ 0.87 1.00 0.13 0.15 0.18 CD19 0.38 0.13 1.00 0.860.74 CD20 0.42 0.15 0.86 1.00 0.74 FCRL5 0.40 0.18 0.74 0.74 1.00

Blood B cell transcript levels measured by RT-qPCR were significantlycorrelated with mRNA levels quantified using Agilent whole-genome geneexpression microarrays (FIG. 1C), however the dynamic range fordetection of low abundance transcripts was significantly extended usingthe RT-qPCR method. This was important for the overall strategy of usingthese assays for the detection and quantitation of rare B lineage cellsin whole blood. For the results shown in FIG. 1C, whole blood RNAs frompatients receiving B cell depletion therapy at baseline (n=10), day 15(n=10) and day 84 (n=10) were assayed for IgJ using RT-qPCR (y axis) andby Agilent whole genome mRNA microarray analysis (x axis), and a Pearsoncorrelation coefficient was calculated.

Baseline IgJ and FCRL5 mRNA Levels as Biomarkers for Rituximab Response

The REFLEX trial of rituximab therapy in anti-TNF inadequate responders(Cohen S B, et al., Arthritis Rheum. 2006; 54 (9): 2793-806) was used asa training set to identify baseline mRNA biomarkers predictive oftreatment response. Baseline RNA was available from 141 REFLEX studyparticipants (118 in the rituximab treatment arm, 23 in the placeboarm). Clinical and laboratory data at baseline for the REFLEX cohort areprovided in Table 2. There were no significant differences in baselineparameters between the training set studied here and the overall REFLEXstudy population (Table 3).

TABLE 2 Baseline clinical and demographic data for the REFLEX, DANCER,SERENE and SCRIPT RA cohorts. REFLEX DANCER SERENE SCRIPT Baseline N =141 N = 142 N = 151 N = 413 Characteristics Mean ± SD Mean ± SD Mean ±SD P value^(a) Mean ± SD Age (years) 52 ± 12 52 ± 12 49 ± 13 0.044 54 ±11 Gender (% female) 80 82 85 NS 77 RA duration (years) 12 ± 8  11 ± 9 6 ± 6 3.2 × 10⁻¹⁰ 12 ± 9  Rheumatoid Factor (% 76 77 84 NS 92 positive)Swollen Joint Count 14 ± 6  13 ± 5  14 ± 6  NS 18.3 ± 11.8 Tender JointCount 17 ± 7  17 ± 6  15 ± 7  0.022 29.5 ± 15.8 DAS28 6.8 ± 0.9 6.7 ±0.8 6.5 ± 1   0.036 6.0 ± 1.0 C-Reactive Protein 3.6 ± 4   3.2 ± 4   2 ±2 3.2 × 10⁻⁵  2.6 ± 2.7 (mg/dl) IgG 13 ± 4  12 ± 3  13 ± 4  NS IgM 1.7 ±0.9 1.5 ± 0.7 1.5 ± 0.9 NS IgA 3 ± 2 3 ± 1 3 ± 1 NS ^(a)For continuousvariables, P-values were derived from one way ANOVA. For categoricalvariables, P-values were derived from a X² statistical test. Significantp-values (<0.05) are shown; NS = not signficant. IgG (normal range5.5-16.5 g/L), IgM (normal range 0.4-2.0 g/L), IgA (normal range 0.8-4.0g/L).

TABLE 3 Baseline demographics and clinical features in sampled subsetsas compared to the overall trial populations. REFLEX DANCER SERENESCRIPT Baseline All Sample All Sample All Sample All SampleCharacteristics N = 518 N = 141 N = 462 N = 142 N = 509 N = 151 N = 840N = 413 Age (years) 52 ± 12 52 ± 12 51 ± 12 52 ± 12 52 ± 13 49 ± 13 54 ±11 54 ± 11 Gender (% female) 82 80 81 82 82 85 80 77 RA duration (years)12 ± 8  12 ± 7  10 ± 8  11 ± 9  7 ± 7 6 ± 5 12 ± 9  12 ± 9  Rheumatoidfactor (%) 76 76 80 77 86 84 89 92 Swollen joint count 14.7 ± 5.9  14.3± 5.9  13.9 ± 5.6  13.4 ± 5.1  13.1 ± 5.6  13.4 ± 5.9  17.0 ± 11.3 18.3± 11.8 (28 joints assessed) Tender joint count 17.0 ± 7.1  16.9 ± 7.2 17.6 ± 6.4  16.7 ± 6.4  15.0 ± 6.8  14.9 ± 7.1  26.2 ± 15.7 29.5 ± 15.8(28 joints assessed) DAS28 6.9 ± 1.0 6.8 ± 0.9 6.8 ± 0.9 6.7 ± 0.9 6.5 ±1.0 6.5 ± 1.0 5.9 ± 1.1 6.0 ± 1.0 CD19 (cells/ul) 197 ± 157 201 ± 189174 ± 143 162 ± 117 199 ± 171 228 ± 145 C-Reactive Protein 3.8 ± 3.9 3.6± 3.6 3.1 ± 3.2 3.2 ± 3.6 2.1 ± 2.3 2.0 ± 1.9 2.8 ± 2.9 2.6 ± 2.7(mg/dl) IgG* 13 ± 4  13 ± 4  13 ± 4  12 ± 3  14 ± 4  13 ± 4  IgM* 1.6 ±0.9 1.7 ± 0.8 1.6 ± 0.8 1.5 ± 0.7 1.5 ± 0.8 1.5 ± 0.9 IgA* 3 ± 1 3 ± 1 3± 1 3 ± 1 3 ± 1 3 ± 2 *IgG (normal range 5.5-16.5 g/L), IgM (normalrange 0.4-2.0 g/L), IgA (normal range 0.8-4.0 g/L).

The ACR50 response rate at 24 weeks, which denotes a 50% improvement insigns and symptoms of active RA, was used as the primary outcome measurefor this study. The ACR50 rate in the active arm of the REFLEX patientcohort for which mRNA samples were available was 25%, compared with 17%in the placebo arm. In comparison, the overall REFLEX trial populationhad an ACR50 rate of 27% in the active arm (n=298), and 5% in theplacebo arm (n=201).

Baseline IgJ mRNA levels assayed by RT-qPCR in whole blood were comparedin ACR50 nonresponders (n=88) and responders (n=30) from the active armof the REFLEX trial of rituximab in RA. As shown in FIG. 1D, meanbaseline mRNA expression levels of IgJ (and BCMA, data not shown) wereslightly higher in patients who failed to achieve ACR50 response ratesat week 24 (P=0.03), and there was a significant enrichment of ACR50nonresponders in the subgroup of patients with baseline IgJ above athreshold of 0.1 mRNA expression units. There were no statisticallysignificant differences in baseline expression of CD20, CD19 or FCRL5between the two patient subgroups (data not shown). Formal thresholdanalysis indicated that baseline IgJ and BCMA expression had the bestability to distinguish between ACR50 responders and non-responders (seebelow). In contrast, as shown in FIGS. 2A and B, CD19 and FCRL5 (alsoCD20, data not shown), as single baseline markers, did not significantlystratify the population for response. Biomarker thresholds wereestablished using a formal threshold analysis technique as described inthe Methods above.

We next applied the IgJ^(hi) biomarker to the available samples from twoadditional independent rituximab RA studies, DANCER (Emery et al.,Arthritis Rheum. 2006; 54:1390-1400) and SERENE (Emery et al., Ann.Rheum. Dis. 2010; 69:1629-1635), and the ocrelizumab RA study SCRIPT.DANCER was a phase II study that enrolled both TNF-inadequate responders(TNF-IR) and methotrexate-IR (MTX-IR) subjects, SERENE was a phase IIIstudy that enrolled only MTX-IR subjects, and SCRIPT was a phase IIIstudy that enrolled TNF-IR subjects (see Methods above). Together, thethree replication cohorts comprised 475 anti-CD20-treated (297 TNF-IRand 178 MTX-IR) and 228 placebo-treated (144 TNF-IR and 84 MTX-IR)subjects. Analysis of baseline clinical and demographic data showed agenerally balanced distribution of subject age, gender, andseropositivity between the replication cohorts and the original REFLEXtest cohort (Table 2). The observed baseline differences in diseaseduration, tender, and swollen joint counts and CRP reflected individualtrial inclusion criteria (Table 2).

As shown in FIG. 3, an RA subgroup was defined by an IgJ mRNA biomarkerthat demonstrated reduced efficacy after anti-CD20 therapy. FIG. 3Ashows the identification of optimal biomarker thresholds for IgJ as apredictor of ACR50 response rates at 6 months (day 168) followingassessment of baseline mRNA samples from the REFLEX trial of rituximabin RA. In FIGS. 3A-D, subjects treated with anti-CD20 are indicated byhatched bars; subjects who received placebo are indicated by open bars.The biomarker threshold (IgJ≧ or <0.1 expression units) was then testedprospectively in baseline mRNA samples from the DANCER and SERENE trialsof rituximab in RA. Biomarker thresholds for the SCRIPT trial ofocrelizumab in RA were based on percentage thresholds from rituximabstudies.

Application of the pre-established IgJ single biomarker threshold(IgJ≧0.1 units) to DANCER resulted in a 16% enrichment of ACR50 ratesfor the IgJ^(lo) subset (30% in IgJ^(lo) vs. 14% in IgJ^(hi); FIG. 3B),and a 6% enrichment in SERENE (30% in IgJ^(lo) vs. 24% in IgJ^(hi); FIG.3C). For SCRIPT, non-amplified RNA was used for the biomarker assays andthus the precise expression threshold established in REFLEX could not beapplied to SCRIPT samples. Instead, the pre-determined overallpercentage threshold from the rituximab studies IgJ^(hi) defined as thetop 20% of samples—was applied prospectively to the SCRIPT IgJ biomarkeranalysis. Using this threshold, there was a 15% enrichment in ACR50rates in the SCRIPT IgJ^(lo) as compared to the IgJ^(hi) subset (25% inIgJ^(lo) vs. 10% in IgJ^(hi); FIG. 3D). In FIGS. 3A-D, A denotes theACR50 percentage difference for the active anti-CD20 arm between theIgJ^(hi) and IgJ^(lo) subgroups, “n” refers to the number of individualsubjects I each subgroup, and the number above the bars is the % ACR50for each subgroup. FIG. 3E shows odds ratios and 95% c.i. for theenrichment of ACR50 responses in the IgJ^(lo) subgroup as compared tothe IgJ^(hi) subgroup for the individual trials, the replication trialsin aggregate (DANCER, SERENE and SCRIPT), and for all trials together.Each of the trials showed similar trends of improved ACR50 rates in theIgJ^(lo) as compared to IgJ^(hi) subsets (biomarker odds ratios for thefour trials were 4.4, 2.6, 1.4 and 2.9 for REFLEX, DANCER, SERENE andSCRIPT, respectively). In a combined analysis of the three replicationcohorts (DANCER, SERENE and SCRIPT), the overall ACR50 response rate was27% for the IgJ^(lo) group (n=385) and 13% for the IgJ^(hi) group (n=90)(P_(REPLICATION)=0.006; OR=2.4, 95% c.i. (1.2, 5.0); FIG. 2E), withnon-significant differences between the placebo arms (9% and 8%,respectively; P=1.0). When all four trials were combined, the ACR50response rate in the active arms was 28% for the IgJ^(lo) group (n=471)and 12% for the IgJ^(hi) group (n=122) (OR=2.7; 95% c.i. (1.5, 5.3);FIG. 3E).

Having established that a single plasmablast biomarker could enrich foranti-CD20 non-responders across these trials, we next sought todetermine whether a second biomarker could further increase the testpredictive value. The combination of IgJ and BCMA, both plasmablastmarkers, showed no further significant enrichment over IgJ alone (datanot shown). However, the combination of IgJ≧0.1 (IgJ^(hi)) and lowlevels of FCRL5 (<0.02,) FCRL5^(lo)) excluded all the ACR50 respondersin the active arm as shown in FIG. 4A. The response rates for the twobiomarker-defined groups (IgJ^(hi)FCRL5^(lo)) vs. all others) werehighly different (0% ACR50 for IgJ^(hi)FCRL5^(lo), 30% ACR50 for allothers). Subsetting the placebo arm using the two-biomarker combinationresulted in similar ACR50 response rates, suggesting that this biomarkercombination was predictive, rather than prognostic, for response torituximab (FIG. 4A). An IgJ^(hi)CD19^(lo) biomarker combination showedsimilar ability to discriminate subsets for ACR50 (FIG. 2C) and otheroutcome measures (not shown), suggesting that the combination of highlevels of plasmablast mRNA and low levels of naïve/memory B cell mRNA atbaseline was a negative predictor of efficacy for anti-CD20.

Application of the IgJ^(hi)/FCRL5^(lo) combination biomarker thresholdsto the samples from DANCER, SERENE, and SCRIPT resulted in enrichedACR50 response rates in the biomarker negative subsets (FIGS. 4, B, Cand D, respectively). For the rituximab trials, the IgJ^(hi)FCRL5^(lo)biomarker was defined as IgJ expression≧0.1 and FCRL5 expression<0.02.For SCRIPT, the combination biomarker was based on pre-definedpercentage thresholds based on the rituximab studies: IgJ^(hi)—highest20th percentile; FCRL5^(lo)—the lowest 15th percentile. The “All Others”subgroups were comprised of those individuals in each trial who wereIgJ^(lo) together with those who were IgJ^(hi)FCRL5^(hi) “n” refers tothe number of individual subjects in each subgroup, and the number abovethe bars is the % ACR50 for each subgroup. For the replication samples,the overall ACR50 rate in the treatment group was 27% for the biomarkernegative subgroup (n=398) and 12% for the IgJ^(hi)FCRL5^(lo) group(n=74) (P_(REPLICATION)=0.008; OR=2.7, 95% c.i. (1.3, 6.3); FIG. 4E),with non-significant differences between the placebo arms (8% and 11%,respectively; P=0.5). When data from the four trials were combined, theACR50 response rate for the treatment groups was 28% for the biomarkernegative subgroup (n=494) and 9% for the IgJ^(hi)FCRL5^(lo) group (n=95)(OR=3.6, 95% c.i. (1.8, 8.4); FIG. 4E). In total, the IgJ^(hi)FCRL5^(lo)non-responder subgroup comprised 17% of the subjects studied.

Application of the IgJ and IgJ-FCRL5 Biomarkers to Other ClinicalOutcomes

In the combined sample of all four trials, active arm subsets defined byboth the IgJ biomarker (FIGS. 5A-C) and the IgJ-FCRL5 combinationbiomarker (FIGS. 5D-F) also showed differences in ACR20, ACR70, andDAS28 response rates at 6 months. In the figure, hatched bars show theindicated response rates at 6 months (day 168) for patients treated withanti-CD20; open bars show the indicated response rates at 6 months (day168) for patients that received placebo. A in each of the panels denotesthe respective ACR percentage difference for the active anti-CD20 armbetween the IgJ^(lo) and IgJ^(hi) (A-C) subgroups or between all othersand IgJ^(hi)FCRL5^(lo) (D-F). “n” refers to the number of individualpatients in each subgroup, and the number above the bars is the % foreach subgroup. The IgJ^(hi)FCRL5^(lo) subgroup had IgJ expression≧0.1and FCRL5 expression<0.02. The “All Others” subgroups in panels D-F werecomprised of all individuals with baseline IgJ<0.1 plus the individualswho were IgJ≧0.1 and FCRL5≧0.02.

An analysis of baseline clinical and demographic data between thebiomarker defined IgJ^(hi) and IgJ^(lo) subgroups showed that the twosubsets were highly similar (Table 4). Similarly, no significantdifferences were observed in baseline clinical and demographic datadefined by the IgJ-FCRL5 combination biomarker (Table 6). We alsocompared baseline parameters and clinical outcomes for the TNF-IR andMTX-IR subgroups across the three rituximab trials. Consistent with moresevere disease overall, TNF-IR subjects had a longer duration ofdisease, higher CRP levels, and higher baseline DAS28 scores than MTX-IRsubjects (Table 5). Of interest, data from the rituximab studiesindicated that the IgJ^(hi) biomarker subset was enriched in TNF-IR ascompared to MTX-IR subjects (30% vs. 18%, respectively; P=0.01),suggesting the possibility that the IgJ^(hi) subset of RA may also besomewhat resistant to treatment with anti-TNF agents.

TABLE 4 Baseline demographic and clinical data in the IgJ^(lo) andIgJ^(hi) biomarker subgroups^(a). Baseline IgJ^(lo) IgJ^(hi)Characteristics Mean ± SD N Mean ± SD N P-value^(b) Age (years) 52 ± 12667 52 ± 12 180 NS RA duration 10 ± 9  667 11 ± 9  180 NS (years)Swollen joint 16.2 ± 9.7  666 15.7 ± 8.6  180 NS count (28 jointsassessed) Tender Joint 23.0 ± 14.5 666 21.2 ± 11.0 180 NS Count (28joints assessed) DAS28 6.3 ± 1.0 661 6.4 ± 1.1 180 NS C-Reactive 2.9 ±3.0 661 2.4 ± 2.5 179 NS Protein (mg/dl) Baseline Characteristics (%) N(%) N P-value^(c) Gender (% 79 667 84 180 NS female) Rheumatoid 86 61878 171 NS Factor (%) ^(a)Data were pooled from the REFLEX, DANCER,SERENE, and SCRIPT trials. ^(b)2-tailed P- values were derived fromnon-parametric Wilcoxon test. NS—not significant, P ≧ 0.05. ^(c)2-tailedP-values were derived from Fisher Exact test. NS—not significant, P ≧0.05.

TABLE 5 Baseline demographic and clinical data for methotrexate (MTX-IR)and TNF (TNF- IR) inadequate responders from the rituximab studies^(a).MTX-IR TNF-IR N = 262 N = 172 Baseline Characteristics Mean ± SD Mean ±SD P value^(b) Age (years) 51 ± 13 52 ± 12 NS RA duration (years) 8 ± 811 ± 8  1.9 × 10⁻⁸ Swollen joint count (28 joints 13.5 ± 5.5  14.4 ±5.8  NS assessed) Tender Joint Count (28 joints 15.6 ± 6.8  16.9 ± 7.1 NS assessed) DAS28 6.6 ± 0.9 6.8 ± 0.9 0.013 C-Reactive Protein (mg/dl)2.5 ± 2.8 3.5 ± 3.6 1.6 × 10⁻⁵ Baseline Characteristics % % P value^(c)Rheumatoid Factor (%) 82 75 NS Gender (% female) 83 81 NS IgJ^(hi) (%)18 30 0.01  ^(a)Data were pooled from the REFLEX, DANCER and SERENErituximab trials. ^(b)P-values were derived from nonparametric Wilcoxontest. NS—not significant, P ≧ 0.05. ^(c)2-tailed P-values were derivedfrom Fisher Exact test. NS—not significant, P ≧ 0.05.

TABLE 6 Distribution of baseline demographic data between two IgJ/FCRL5biomarker subgroups in all subjects studied. Baseline All OthersIgJ^(hi)FCRL5^(lo) Characteristics Mean ± SD N Mean ± SD N P-value Age(years) 53 ± 12 705 52 ± 12 141 NS RA Duration (years) 11 ± 8  705 10.8± 9.3  141 NS Swollen joint count 16.2 ± 9.6  704 15.6 ± 8.8  141 NS (28joints assessed) Tender joint count 23.0 ± 14.3 704 20.7 ± 11.2 141 NS(28 joints assessed) DAS28 6.4 ± 1.0 699 6.3 ± 1.1 141 NS C-ReactiveProtein 2.8 ± 3.0 699  2.5 ± 2.75 140 NS (mg/dl) BaselineCharacteristics % N % N P-value Rheumatoid factor 86 653 81 135 NS (%)Gender (% female) 82 705 82 141 NS ^(a)Data were pooled from the REFLEX,DANCER, SERENE and SCRIPT trials. P-values were derived from Wilcoxonnon parametric test.

Discussion

Previous studies have attempted to correlate biologic sequelae thatfollow rituximab-induced B cell depletion with clinical outcomes in RA.A persistence of B cells in the peripheral blood in the weeks followingrituximab therapy (Dass S, et al., Arthritis Rheum. 2008; 58 (10):2993-9) or incomplete depletion of synovial B cells at Week 4 (Teng Y K,et al., Arthritis Rheum. 2007; 56 (12): 3909-18) correlated withimpaired response rates in RA. Reconstitution of the B lineage withearly development stage B cells (e.g. CD10+ immature B cells) may be asign of deeper B cell depletion and was associated with better rituximabresponse rates (Leandro M J, et al., Arthritis Rheum. 2006; 54 (2):613-20), whereas reconstitution with memory phenotype B cells (CD27+)was associated with lower response rates (Roll, P., et al., ArthritisRheum. 2008; 58: 1566-1575). The cells that resist B cell depletioninclude B plasmablasts that express surface markers such as CD27 andCD38, but lack CD20 (Palanichamy A, et al., Arthritis Rheum. 2008; 58(12): 3665-3674).

In the current study, we hypothesized that baseline numbers ofCD20-negative plasmablasts might be predictive of response to anti-CD20treatment in RA, and developed RT-qPCR assays to quantitateplasmablast-specific gene expression in whole blood RNA samples toprovide estimates of the cellular composition of blood prior to therapy.Using data and samples from four randomized, placebo controlled studiesof rituximab or ocrelizumab in RA, we found that elevated baselinelevels of the plasmablast-specific transcript IgJ, either as a singlemarker or in combination with low levels of a mature B cell splicevariant of FCRL5, defined a ˜17-20% subpopulation of RA that showedresponse rates that were not different than placebo. Furthermore, thesebiomarkers were not simply prognostic for more severe andtreatment-resistant disease, but rather were predictive markers foranti-CD20 response. Importantly, these are baseline measurements thatcan be made prior to initiation of therapy and have the potential to bestandardized for routine clinical use. Based on the data presented here,we conclude that patients who are positive for the mRNA biomarkersIgJ^(hi) or IgJ^(hi)FCRL5^(lo) at baseline are less likely to receivebenefit from anti-CD20 treatment.

A recent publication provides support for certain conclusions presentedhere (Vital E M, et al., Arthritis Rheum. 2010 May; 62(5):1273-9). In anobservational trial of rituximab outcomes in RA, Vital et al. showedthat the number of baseline plasmablast cells in blood (CD27++CD38++ asdetermined by flow cytometry) was significantly higher in first cyclerituximab non-responders (n=32) as compared to responders (n=54)(OR=0.47; 95% CI 0.28-0.27; P=0.003) (Id.). First cycle rituximabnon-responders were also more likely to have incomplete depletion of Blineage cells following therapy. While the numbers of patients studiedwere relatively small and the data were not from randomized and placebocontrolled subjects, these data nevertheless are consistent with theidea that elevated levels of plasmablasts at baseline predictnon-response to rituximab in RA.

Plasmablasts are not generally found at significant levels in theperipheral blood of healthy individuals, except following vaccination(Odendahl M, et al., Blood. 2005; 105(4): 1614-21) or in the setting ofacute and chronic infections (Jaimes M C, et al., J. Virol. 2004; (20):10967-76; Moir S, et al., Nat Rev Immunol. 2009; 9(4): 235-45). It iscurrently unclear whether circulating plasmablasts have a pathogenicrole in autoimmunity, or are simply markers of a dysregulated andhyperactive immune system. The observation that elevated levels of bloodplasmablasts return towards normal following immunosuppressive therapyin SLE and correlate with improvements in disease activity (Anolik J H,et al., Arthritis Rheum. 2004; 50(11): 3580-90) supports the idea thatplasmablasts may have a role in disease pathogenesis.

Plasmablasts that escape B cell depletion by anti-CD20 may retain theability to home to sites of inflammation (e.g. joints) through theirexpression of chemokine receptors such as CXCR3 and CXCR4 (Hauser A E,et al., J. Immunol. 2002; 169(3): 1277-82). They may then contribute todisease through the local secretion of autoantibodies, which canactivate macrophages via engagement of Fc receptors leading toinflammatory cytokine release (Clavel et al., Arthritis Rheum. 2008;58:678-688). In addition, plasmablasts express high levels of BCMA, ahigh affinity receptor for the survival cytokine BAFF (Yang M, et al.,J. Immunol. 2007; 175(5): 2814-24). The striking elevations of BAFF thatare observed following B cell depletion with anti-CD20 (Cambridge G, etal., Arthritis Rheum 2006; 54:723-732; Vallerskog T, et al., ArthritisRes Ther 2006; 8: R167) may specifically enhance the survival ofcirculating plasmablasts that escape depletion, thereby contributing toresistance to anti-CD20 therapy.

More generally, these data presented here demonstrate the value of largerandomized, placebo-controlled clinical trial datasets for studies thataim to identify baseline biomarkers that can stratify patient subgroupsfor treatment responses. Placebo arms are required for testing theefficacy of new therapies, and they are also essential for determiningwhether biomarkers for defined subgroups are merely prognostic vs.predictive. Prognostic markers stratify patients in terms of diseasecourse or severity, and are not expected to necessarily show significantdifferences between the active and placebo arms. On the other hand,predictive markers stratify the active arm group but not the placeboarm. Predictive markers are valuable for personalized health careapproaches since, once identified, they can assist in the targeting ofindividual drugs to the patients most likely to respond.

In summary, we have shown that elevated baseline blood expression ofplasmablast mRNA markers, either alone or together with low levels ofmature B cell markers, defines a ˜17-20% subset of RA with an impairedresponse to standard B cell depletion therapy with rituximab at 6months. It remains to be determined whether this subset of RA patientswould benefit from additional courses of B cell depletion therapy, orwhether they would respond to alternative available therapies. Inaddition, it will be interesting to determine whether these biomarkerswill be useful in stratifying response rates in other diseases such asmultiple sclerosis, including relapsing-remitting multiple sclerosis(Hauser et al., N Engl. J. Med. 358(7):676-88 (2008)) and primaryprogressive multiple sclerosis (Hawker K, et al., Ann Neurol. 2009October; 66(4):460-71), and ANCA-associated vasculitis (Stone J H, etal., N Engl J. Med. 2010 Jul. 15; 363(3):221-32) where anti-CD20 therapyhas shown clinical activity. Although an FDA-approved (or validated)diagnostic test in not currently available for clinical use, we proposethat determination of baseline plasmablast levels has the potential toinform treatment decisions with anti-CD20 therapeutics in RA in order tomaximize likely clinical benefit.

1. A biomarker for predicting the response of a patient to a therapeuticagent comprising a B-cell antagonist, wherein the biomarker compriseselevated total plasma/plasmablast cell mRNA in a biological sampleobtained from the patient compared to the level of totalplasma/plasmablast cell mRNA in a biological sample obtained from acontrol subject or compared to a threshold value for totalplasma/plasmablast cell mRNA.
 2. The biomarker of claim 1, furthercomprising a low level of total naïve/mature B cell mRNA in thepatient's biological sample compared to the level of total naïve/matureB cell mRNA in the control subject's biological sample or compared to athreshold value for total naïve/mature B cell mRNA.
 3. The biomarker ofclaim 1, wherein the biological sample is whole blood.
 4. The biomarkerof claim 1, wherein the patient is sufferering from, or is suspected ofsuffering from, rheumatoid arthritis.
 5. The biomarker of claim 1,wherein the patient is suffering from, or is suspected of sufferingfrom, an autoimmune disease selected from multiple sclerosis, lupus, andANCA-vasculitis.
 6. The biomarker of claim 5, wherein the multiplesclerosis is selected from relapsing-remitting multiple sclerosis andprimary progressive multiple sclerosis.
 7. The biomarker of claim 1,wherein the B-cell antagonist is selected from an anti-CD22 antibody, ananti-CD20 antibody, an anti-BR3 antibody, and a BR3-Fc immunoadhesin. 8.The biomarker of claim 7, wherein the B-cell antagonist is an anti-CD20antibody.
 9. The biomarker of claim 8, wherein the anti-CD20 antibody isselected from rituximab, ibritumomab tiuxetan, tositumomab, ocrelizumab,1F5, 2H7, and A20.
 10. The biomarker of claim 9, wherein the anti-CD20antibody is rituximab.
 11. The biomarker of claim 9, wherein theanti-CD20 antibody is ocrelizumab.
 12. A biomarker for predicting theresponse of a patient to a therapeutic agent comprising a B-cellantagonist, wherein the biomarker comprises an elevated expression levelof a plasma/plasmablast cell-enriched gene in a biological sampleobtained from the patient compared to the expression level of theplasma/plasmablast cell-enriched gene in a biological sample obtainedfrom a control subject or compared to a threshold value for theplasma/plasmablast cell-enriched gene.
 13. The biomarker of claim 12,further comprising a low expression level of a naïve/mature Bcell-enriched gene in the patient's biological sample compared to theexpression level of the naïve/mature B cell-enriched gene in the controlsubject's biological sample or compared to a threshold value for thenaïve/mature B cell-enriched gene.
 14. The biomarker of claim 12,wherein the plasma/plasmablast cell-enriched gene is IgJ.
 15. Thebiomarker of claim 13, wherein the naïve/mature B cell-enriched gene isFCRL5.
 16. The biomarker of claim 13, wherein the naïve/mature Bcell-enriched gene is CD19.
 17. The biomarker of claim 13, wherein theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is FCRL5.
 18. The biomarker of claim 13, wherein theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is CD
 19. 19. The biomarker of claim 12, wherein thebiomarker comprises mRNA.
 20. The biomarker of claim 12, wherein thebiological sample is whole blood.
 21. The biomarker of claim 12, whereinthe patient is sufferering from, or is suspected of suffering from,rheumatoid arthritis.
 22. The biomarker of claim 12, wherein the patientis suffering from, or is suspected of suffering from, an autoimmunedisease selected from multiple sclerosis, lupus, and ANCA-vasculitis.23. The biomarker of claim 22, wherein the multiple sclerosis isselected from relapsing-remitting multiple sclerosis and primaryprogressive multiple sclerosis.
 24. The biomarker of claim 12, whereinthe B-cell antagonist is selected from an anti-CD22 antibody, ananti-CD20 antibody, an anti-BR3 antibody, and a BR3-Fc immunoadhesin.25. The biomarker of claim 24, wherein the B-cell antagonist is ananti-CD20 antibody.
 26. The biomarker of claim 25, wherein the anti-CD20antibody is selected from rituximab, ibritumomab tiuxetan, tositumomab,ocrelizumab, 1F5, 2H7, and A20.
 27. The biomarker of claim 26, whereinthe anti-CD20 antibody is rituximab.
 28. The biomarker of claim 26,wherein the anti-CD20 antibody is ocrelizumab.
 29. The biomarker ofclaim 17, wherein the patient is sufferering from, or is suspected ofsuffering from, rheumatoid arthritis, and wherein the B-cell antagonistis selected from rituximab and ocrelizumab.
 30. The biomarker of claim17, wherein the patient is suffering from, or is suspected of sufferingfrom, an autoimmune disease selected from multiple sclerosis, lupus, andANCA-vasculitis, and wherein the B-cell antagonist is selected fromrituximab and ocrelizumab.
 31. The biomarker of claim 30, wherein themultiple sclerosis is selected from relapsing-remitting multiplesclerosis and primary progressive multiple sclerosis.
 32. The biomarkerof claim 1 or claim 12, wherein the predicted response is non-response.33. A method of predicting the response of a patient to a therapycomprising a B-cell antagonist, the method comprising: measuring in abiological sample obtained from the patient the expression of at leastone gene enriched in plasma/plasmablast cells and comparing theexpression of the at least one gene in the patient's biological sampleto the expression of the same at least one gene in a biological sampleobtained from a control subject or to a threshold value for the at leastone plasma/plasmablast cell-enriched gene, wherein elevated expressionof the at least one gene in the patient's biological sample compared tothe expression in the control subject's biological sample or to thethreshold value is predictive of response of the patient to the therapycomprising the B-cell antagonist.
 34. The method of claim 33, furthercomprising: measuring in the biological sample obtained from the patientthe expression of at least one gene enriched in naïve/mature B cells andcomparing the expression of the at least one naïve/mature Bcell-enriched gene in the patient's biological sample to the expressionof the same at least one naïve/mature B cell-enriched gene in thebiological sample obtained from the control subject or to a thresholdvalue for the naïve/mature B cell-enriched gene, wherein a low level ofexpression of the at least one naïve/mature B cell-enriched gene in thepatient's biological sample compared to the expression of the same atleast one naïve/mature B cell-enriched gene in the control subject'sbiological sample or to the threshold value for the naïve/mature Bcell-enriched gene is predictive of response of the patient to thetherapy comprising the B-cell antagonist.
 35. The method of claim 33,wherein the plasma/plasmablast cell-enriched gene is IgJ.
 36. The methodof claim 34, wherein the naïve/mature B cell-enriched gene is FCRL5. 37.The method of claim 34, wherein the naïve/mature B cell-enriched gene isCD19.
 38. The method of claim 34, wherein the plasma/plasmablastcell-enriched gene is IgJ and the naïve/mature B cell-enriched gene isFCRL5.
 39. The method of claim 34, wherein the plasma/plasmablastcell-enriched gene is IgJ and the naïve/mature B cell-enriched gene isCD
 19. 40. The method of claim 33, wherein measuring the expression ofat least one gene comprises measuring mRNA.
 41. The method of claim 40,wherein measuring mRNA comprises a PCR method or a microarray chip. 42.The method of claim 33, wherein the biological sample comprises wholeblood.
 43. The method of claim 33, wherein the patient is sufferingfrom, or is suspected of suffering from, rheumatoid arthritis.
 44. Themethod of claim 33, wherein the patient is suffering from, or issuspected of suffering from, an autoimmune disease selected frommultiple sclerosis, lupus, and ANCA-vasculitis.
 45. The method of claim44, wherein the multiple sclerosis is selected from relapsing-remittingmultiple sclerosis and primary progressive multiple sclerosis.
 46. Themethod of claim 33, wherein the B-cell antagonist is selected from ananti-CD22 antibody, an anti-CD20 antibody, an anti-BR3 antibody, and aBR3-Fc immunoadhesin.
 47. The method of claim 46, wherein the B-cellantagonist is an anti-CD20 antibody.
 48. The method of claim 47, whereinthe anti-CD20 antibody is selected from rituximab, ibritumomab tiuxetan,tositumomab, ocrelizumab, 1F5, 2H7, and A20.
 49. The method of claim 48,wherein the anti-CD20 antibody is rituximab.
 50. The method of claim 48,wherein the anti-CD20 antibody is ocrelizumab.
 51. The method of claim38, wherein the patient is sufferering from, or is suspected ofsuffering from, rheumatoid arthritis, and wherein the B-cell antagonistis selected from rituximab and ocrelizumab.
 52. The method of claim 38,wherein the patient is suffering from, or is suspected of sufferingfrom, an autoimmune disease selected from multiple sclerosis, lupus, andANCA-vasculitis, and wherein the B-cell antagonist is selected fromrituximab and ocrelizumab.
 53. The method of claim 52, wherein themultiple sclerosis is selected from replasing-remitting multiplesclerosis and primary progressive multiple sclerosis.
 54. The method ofclaim 39, wherein the patient is sufferering from, or is suspected ofsuffering from, rheumatoid arthritis, and wherein the B-cell antagonistis selected from rituximab and ocrelizumab.
 55. The method of claim 39,wherein the patient is suffering from, or is suspected of sufferingfrom, an autoimmune disease selected from multiple sclerosis, lupus, andANCA-vasculitis, and wherein the B-cell antagonist is selected fromrituximab and ocrelizumab.
 56. The method of claim 55, wherein themultiple sclerosis is selected from replasing-remitting multiplesclerosis and primary progressive multiple sclerosis.
 57. The method ofclaim 33, wherein the predicted response is non-response.
 58. A methodof treating rheumatoid arthritis in a patient comprising administering atherapeutically effective amount of a therapeutic agent other than aB-cell antagonist to the patient to treat the rheumatoid arthritis,provided that a biological sample obtained from the patient has beenshown to possess elevated expression of at least one gene enriched inplasma/plasmablast cells compared to the expression level of the same atleast one gene in a biological sample obtained from a control subject orto a threshold value for the plasma/plasmablast cell-enriched gene. 59.The method of claim 58, wherein the biological sample has in additionbeen shown to possess a low level of expression of at least one geneenriched in naïve/mature B cells compared to the expression level of thesame at least one gene enriched in naïve/mature B cells in thebiological sample obtained from the control subject or to a thresholdvalue for the naïve/mature B cell-enriched gene.
 60. The method of claim58, wherein the plasma/plasmablast cell-enriched gene is IgJ.
 61. Themethod of claim 59, wherein the naïve/mature B cell-enriched gene isFCRL5.
 62. The method of claim 59, wherein the naïve/mature Bcell-enriched gene is CD19.
 63. The method of claim 59, wherein theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is FCRL5.
 64. The method of claim 59, wherein theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is CD
 19. 65. The method of claim 58, wherein thebiological sample comprises whole blood.
 66. A method of treatingmultiple sclerosis in a patient comprising administering atherapeutically effective amount of a therapeutic agent other than aB-cell antagonist to the patient to treat the multiple sclerosis,provided that a biological sample obtained from the patient has beenshown to possess elevated expression of at least one gene enriched inplasma/plasmablast cells compared to the expression level of the same atleast one gene in a biological sample obtained from a control subject orto a threshold value for the plasma/plasmablast cell-enriched gene. 67.The method of claim 66, wherein the biological sample has in additionbeen shown to possess a low level of expression of at least one geneenriched in naïve/mature B cells compared to the expression level of thesame at least one gene enriched in naïve/mature B cells in a biologicalsample obtained from a control subject or to a threshold value for thenaïve/mature B cell-enriched gene.
 68. The method of claim 66, whereinthe plasma/plasmablast cell-enriched gene is IgJ.
 69. The method ofclaim 67, wherein the naïve/mature B cell-enriched gene is FCRL5. 70.The method of claim 67, wherein the naïve/mature B cell-enriched gene isCD19.
 71. The method of claim 67, wherein the plasma/plasmablastcell-enriched gene is IgJ and the naïve/mature B cell-enriched gene isFCRL5.
 72. The method of claim 67, wherein the plasma/plasmablastcell-enriched gene is IgJ and the naïve/mature B cell-enriched gene isCD
 19. 73. The method of claim 66, wherein the biological samplecomprises whole blood.
 74. The method of claim 66, wherein the multiplesclerosis is selected from relapsing-remitting multiple sclerosis andprimary progressive multiple sclerosis.
 75. A method of treatingANCA-vasculitis in a patient comprising administering a therapeuticallyeffective amount of a therapeutic agent other than a B-cell antagonistto the patient to treat the ANCA-vasculitis, provided that a biologicalsample obtained from the patient has been shown to possess elevatedexpression of at least one gene enriched in plasma/plasmablast cellscompared to the expression level of the same at least one gene in abiological sample obtained from a control subject or to a thresholdvalue for the plasma/plasmablast cell-enriched gene.
 76. The method ofclaim 75, wherein the biological sample has in addition been shown topossess a low level of expression of at least one gene enriched innaïve/mature B cells compared to the expression level of the same atleast one gene enriched in naïve/mature B cells in a biological sampleobtained from a control subject or to a threshold value for thenaïve/mature B cell-enriched gene.
 77. The method of claim 75, whereinthe plasma/plasmablast cell-enriched gene is IgJ.
 78. The method ofclaim 76, wherein the naïve/mature B cell-enriched gene is FCRL5. 79.The method of claim 76, wherein the naïve/mature B cell-enriched gene isCD19.
 80. The method of claim 76, wherein the plasma/plasmablastcell-enriched gene is IgJ and the naïve/mature B cell-enriched gene isFCRL5.
 81. The method of claim 76, wherein the plasma/plasmablastcell-enriched gene is IgJ and the naïve/mature B cell-enriched gene isCD
 19. 82. The method of claim 75, wherein the biological samplecomprises whole blood.
 83. A method of treating lupus in a patientcomprising administering a therapeutically effective amount of atherapeutic agent other than a B-cell antagonist to the patient to treatthe lupus, provided that a biological sample obtained from the patienthas been shown to possess elevated expression of at least one geneenriched in plasma/plasmablast cells compared to the expression level ofthe same at least one gene in a biological sample obtained from acontrol subject or to a threshold value for the plasma/plasmablastcell-enriched gene.
 84. The method of claim 83 wherein the biologicalsample has in addition been shown to possess a low level of expressionof at least one gene enriched in naïve/mature B cells compared to theexpression level of the same at least one gene enriched in naïve/matureB cells in a biological sample obtained from a control subject or to athreshold value for the naïve/mature B cell-enriched gene.
 85. Themethod of claim 83, wherein the plasma/plasmablast cell-enriched gene isIgJ.
 86. The method of claim 84, wherein the naïve/mature Bcell-enriched gene is FCRL5.
 87. The method of claim 84, wherein thenaïve/mature B cell-enriched gene is CD19.
 88. The method of claim 84,wherein the plasma/plasmablast cell-enriched gene is IgJ and thenaïve/mature B cell-enriched gene is FCRL5.
 89. The method of claim 84,wherein the plasma/plasmablast cell-enriched gene is IgJ and thenaïve/mature B cell-enriched gene is CD
 19. 90. The method of claim 83,wherein the biological sample comprises whole blood.
 91. A method ofselecting a therapeutic agent for treatment of a patient suffering froman autoimmune disease comprising: obtaining a biological sample from thepatient; measuring in the biological sample obtained from the patientthe expression of at least one gene enriched in plasma/plasmablastcells; comparing the expression of the at least one gene in thepatient's biological sample to the expression of the same at least onegene in a biological sample obtained from a control subject or to athreshold value for the at least one plasma/plasmablast cell-enrichedgene; determining whether the expression of the at least one gene in thepatient's biological sample is elevated compared to the expression inthe control subject's biological sample or to the threshold value; andselecting a therapeutic agent other than a B-cell antagonist providedthe expression of the at least one gene in the patient's biologicalsample is elevated.
 92. The method of claim 91, further comprising:measuring in the biological sample obtained from the patient theexpression of at least one gene enriched in naïve/mature B cells;comparing the expression of the at least one naïve/mature Bcell-enriched gene in the patient's biological sample to the expressionof the same at least one naïve/mature B cell-enriched gene in thebiological sample obtained from the control subject or to a thresholdvalue for the naïve/mature B cell-enriched gene; determining whether theexpression of the at least one naïve/mature B cell-enriched gene in thepatient's biological sample is low compared to the expression in thesame at least one naïve/mature B cell-enriched gene in the controlsubject's biological sample or to the threshold value for thenaïve/mature B cell-enriched gene; and selecting a therapeutic agentother than a B-cell antagonist provided the expression of the at leastone naïve/mature B cell-enriched gene is low.
 93. The method of claim91, wherein the plasma/plasmablast cell-enriched gene is IgJ.
 94. Themethod of claim 92, wherein the naïve/mature B cell-enriched gene isFCRL5.
 95. The method of claim 92, wherein the naïve/mature Bcell-enriched gene is CD19.
 96. The method of claim 92, wherein theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is FCRL5.
 97. The method of claim 92, wherein theplasma/plasmablast cell-enriched gene is IgJ and the naïve/mature Bcell-enriched gene is CD
 19. 98. The method of claim 91, whereinmeasuring the expression of at least one gene comprises measuring mRNA.99. The method of claim 98, wherein measuring mRNA comprises a PCRmethod or a microarray chip.
 100. The method of claim 91, wherein thebiological sample comprises whole blood.
 101. The method of claim 91,wherein the autoimmune disease is selected from rheumatoid arthritis,multiple sclerosis, relapsing-remitting multiple sclerosis, primaryprogressive multiple sclerosis, lupus, and ANCA-vasculitis.